BIO 260 – GENETICS REVIEW & STUDY QUESTIONS.1
                                                  Fall 2007
                ...
Genes: A Mendelian View Chapter 3

1. Discuss the significance of Mendel’s work and the virtues of Pisum sativum.
2. What ...
15. Describe the process of DNA replication; include the role of helicases, primase, replication origins,
    DNA polymera...
18. Describe the general features of transcription in eukaryotes.
19. Describe a typical eukaryotic promoter. What are the...
Techniques of Gene Cloning and Recombinant DNA: Chapters 19

1. Define recombinant DNA (rDNA) and discuss how it has revol...
PART II

Extensions of Mendelian Inheritance: Sex Chromosomes, Multiple Alleles, Epistasis, , etc.
Chapters 7 & 4

1.    D...
Genetic Mapping Using Linkage Analysis: Chapter 5

1.    What is genetic linkage and how is it determined?
2.    How do yo...
Introduction to Bacterial and Viral Genetics: Chapter 6

1. Why are bacteria so useful to genetics and why were they not u...
13. Describe how methylation may be correlated with gene expression and chromatin structure.
14. What are the functions, c...
PART III

Applications of rDNA: Genomics, Transgenics, Gene Therapy, etc. Chapters 19 & 20

1. What is genomics and why is...
5.    Define and describe the concept of the prokaryotic operon.
6.    Describe the structure of the lactose operon; inclu...
Population Genetics Chapter 25

1. Describe allelic variation in populations. What molecular techniques are used to detect...
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BIO 260 – GENETICS REVIEW

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BIO 260 – GENETICS REVIEW

  1. 1. BIO 260 – GENETICS REVIEW & STUDY QUESTIONS.1 Fall 2007 Dr. Christopher Harendza PART I Introduction to Genetics Chapter 1 1. Name and define the main areas of genetic research and give an example of each. 2. Review and know the scientific method and the steps involved in formulation of a theory. 3. Beginning with Aristotle and ending with the present, provide a brief overview of the major historical events in the field of genetics. 4. What are some characteristics that are desirable to have in model genetic research organisms? 5. Cite the virtues of the main organisms that are commonly used today in genetic research; include E. coli, Saccharomyces cerevesiae, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana and Mus musculus. 6. Read and review chapter 1 – much of this is general biological knowledge discussed in prerequisite courses. Meiosis & Chromosomes Chapter 2 1. Note that most of p. 18-27 is review from BIO 151. This is not a cell biology course and you should know all stages in the eukaryotic cell cycle; including mitotic stages and the fundamental differences between mitosis and meiosis. We will not be discussing this in class. 2. Review and know the difference between prokaryotic and eukaryotic organisms regarding cell structure, chromosome structure and means of reproduction. 3. What are the fundamental differences and the general steps of mitosis and meiosis? 4. Know the fine detailed structures of replicated chromosomes, including chromatid, centromere, telomere, satellite, secondary constrictions, etc. 5. Compare and contrast between metacentric, submetacentric, acrocentric and telocentric chromosomes. 6. Know the concepts of karyotyping and its utility; include euchromatin, heterochromatin (facultative and constitutive). 7. Know the details of karyotyping in Homo sapiens. Distinguish between amniocentesis and chorionic villus sampling. Also, know the nomenclature for human chromosomes, including p and q arms, regions and bands (e.g. G bands), e.g. 7 q 31. 8. Understand the concepts of ploidy, diploid, haploid, monoploid chromosome sets, polyploid, aneuploid as well as the proper nomenclature describing homologous chromosomes. 9. Outline the all steps of meiosis, and the discuss the function of each step. 10. Know the importance of prophase I, and its substages (leptotene, zygotene, pachytene and diakinesis etc.) in detail. 11. Explain how the events of meiosis provide the physical basis for Mendel's rules. 12. Relate the events of meiosis to Mendel’s law of independent assortment. 13. Understand/review gametogenesis in plants and animals; include and know all terminology. We will not be discussing this in the class. 14. Know the life cycle of yeast, using Saccharomyces cerevesiae as the paradigm, paying attention to the 1N and 2N states. 15. Answer all relevant problems and perform the genetic media lab activities at the end of the chapter (CD and or web site). 1 This is a basic list of review and study questions; recognize that there will be numerous other content objectives discussed during the unit. In addition, your patience in dealing with the difficulties of working with a brand new text is greatly appreciated!
  2. 2. Genes: A Mendelian View Chapter 3 1. Discuss the significance of Mendel’s work and the virtues of Pisum sativum. 2. What are the principles of segregation and independent assortment, and how did Mendel discover them? 3. Understand how to predict the genotypes and phenotypes of progeny from a dihybrid cross using probability, the Punnet square, or the branched-line method. 4. Understand how to predict the genotypes and phenotypes of progeny from trihybrid and multihybrid crosses using the branched-line method and probabilities. 5. Be able to apply a chi-square test to determine goodness of fit. 6. Understand how to use the binomial theory to determine complex probabilities. Note that we will limit this to single factor inheritance in this course, e.g. for genetic counseling. Also, the single step binomial formula will be given but you must know how to symbols and how to use it. 7. Understand the genetic nomenclature of wild types, of alleles, and of crosses; including the accepted methods for Drosophila. 8. Understand the elementary principles of probability; the product rule and the sum rule, and how to use them in genetic calculations. 9. Understand how to interpret a pedigree and how to assign probabilities of genotypes and phenotypes to specific members of the pedigree. 10. Understand how to use a pedigree to predict the genotypes and phenotypes of potential offspring of individuals in the pedigree. We will not get into complex probabilities due to inbreeding. 11. Answer all relevant problems and perform the genetic media lab activities at the end of the chapter (CD and or web site). Genes: A Molecular View - DNA Structure, Replication & Recombination Chapters 10 & 11 1. Understand that many of the details of DNA structure and replication are issues of biochemistry and that we will not dwell on these issues. The segment on DNA structure and history will be presented as a Screenwatch™ Powerpoint / Podcast. You must view this information out of class on your own time. You are responsible for this information, as it was discussed in fairly great detail in BIO 151. 2. Describe the classic experiments using Streptococcus pneumoniae and mice that were performed by Fred Griffith’s and explain how they support the theory that DNA and not protein is the genetic material. 3. Describe how Avery, McLeod and McCarty utilized partially purified enzymes and purified DNA to expand upon Griffith’s experiments. 4. Describe the classic Hershey Chase experiments with T4 bacteriophage. 5. Know the viral reproductive cycle. 6. Provide a historical context of three events above with respect to modern world history and humankind’s entry into the modern age, i.e. what technologies (and wars) were involved here? 7. Know the basic structure of nucleic acids and describe the NA that are found in DNA. 8. Know which bases are purines and pyrimidines. Which are larger? 9. Describe the analyses performed by Chargoff and discuss their significance. 10. What is X-ray diffraction? 11. Describe the work of Wilkins, Franklin, Watson and Crick. 12. Describe the structure and characteristics of DNA molecules; include 5’ , 3’, sugar-phosphate backbone, phosphodiester bond, antiparallel, sense, non-sense, major groove, minor groove, etc. 13. Describe the basis and importance of complementary base pairing. Which base pair is more stable 14. Discuss how the structure of DNA allows the molecule to replicate. 2
  3. 3. 15. Describe the process of DNA replication; include the role of helicases, primase, replication origins, DNA polymerases, leading strand, lagging strand, Okazaki fragments, replication fork, DNA ligase, etc. 16. Discuss the enzymatic specificity of DNA replication. 17. List and know the functions of the multiple DNA polymerases of prokaryotes and eukaryotes. Who was Arthur Kornberg and what did he do? 18. Describe, in detail, the experiments performed by Meselson and Stahl which provided evidence that DNA replication is semiconservative. 19. Compare the replication of small circular genomes, such as those of bacteria vs. large linear genomes such as those of mammals. 20. Discuss how the development in bacterial and viral genetics led to the development of “recombinant DNA technology.” 21. Explain the subtle differences between molecular genetics, molecular biology and recombinant DNA technology. 22. Distinguish between generalized, site specific / homologous and non-homologous recombination. 23. Describe the mechanism proposed for homologous recombination, include heteroduplex DNA, Holliday structures, etc. 24. Define gene conversion and discuss its significance. 25. Understand the details of the DNA isolation procedure; include the role of PCIA, sodium acetate, alcohol, UV spectrophotometry, etc. etc. 26. Answer all relevant problems and perform the genetic media lab activities at the end of the chapter (CD and or web site). How Genes Work: Transcription, the Genetic Code & Translation: Chapters 13 & 14 1. Understand that many of the details of the mechanisms of transcription and translation are largely issues of biochemistry and that we will not dwell on these issues, as these topics are discussed in fairly great detail in BIO 151. You are certainly responsible for this information. 2. Although you need to respect the previous point, it is of even greater importance, as far as this course is concerned, that the fundamental issues surrounding most of these mechanisms were first identified via a mutational analysis, predominantly in E. coli. 3. Discuss the experiments behind the "one gene-one enzyme” and “one gene one polypeptide” theories. Who did these experiments? 4. Distinguish between mRNA, tRNA, rRNA and snRNA with respect to size, stability and function, as well as the pertinent issues regarding their genes. 5. List all of the differences between DNA and RNA and discuss their significance. 6. Do all genes encode proteins? What are the exceptions and what are their functions? 7. Describe the process of transcription of DNA into mRNA; include the roles of RNA polymerase, transcription factors, melting, template strand, (+) strand, (-) strand, 5’, 3’, downstream, upstream etc. Be aware of the other terms used to describe the strandedness of genes, e.g. sense, antisense, etc. 8. Describe the general features of transcription in prokaryotes. 9. Describe RNA polymerase in E. coli. Describe its enzymatic directionality. 10. What is/are the function of (sigma factors)? 11. Describe a typical prokaryotic promoter, including the –35 and – 10 sequences. What it meant by “-35” and “-10”? 12. What is a “consensus sequence?” 13. What is a polycistronic mRNA? Why are they (typically) not found in eukaryotes? 14. Discuss the coupling of transcription and translation in prokaryotes. 15. Describe the process of transcription termination in prokaryotes. 16. Describe the structure of a typical eukaryotic gene. 17. Describe the multiple RNA polymerases in eukaryotes. 3
  4. 4. 18. Describe the general features of transcription in eukaryotes. 19. Describe a typical eukaryotic promoter. What are the functions of the UPE and TATA box? 20. What are enhancers and how are they thought to operate? How do they behave (with respect to directionality and distance from “+1”). Why are they so useful in transgenic farm animals? 21. What is the structure and function of the 5’ cap of eukaryotic mRNAs? 22. Why are eukaryotic genes so large when compared to prokaryotic genes? 23. What are introns and why are they thought to exist? What are exons? 24. What is heteroduplex mapping? 25. What are the intron consensus sequences and what are their roles? 26. Describe the process of RNA processing and comment on its fidelity. What is a lariat? 27. What is a self splicing intron? 28. Define ribozyme and discuss the significance of ribozymes. 29. Describe the process of 3’ end formation and polyadenylation of eukaryotic mRNA. 30. What is the function of the poly A tail? 31. How can the poly A tail be used to isolate mRNA? 32. What are UTRs (untranslated regions) of eukaryotic mRNAs and what are their possible functions? 33. Review / describe the genetic code. How are the 4 "letters" of the code used to code for 20 amino acids? Define codon. 34. Provide an overview of the approach that Khorana and Nirenberg took to “crack” the genetic code. 35. Comment on the "universal" nature of the genetic code. 36. What are the roles of "start" and "stop" codons? 37. Discuss, in detail, the importance of the degeneracy of the genetic code. Provide examples. 38. Discuss the organization of the genetic code table from the standpoint of the groupings of the four main classes of amino acids. 39. Be able to "transcribe" any DNA sequence into RNA and "translate", using a table of the genetic code, any RNA sequence into protein. 40. What is “codon preference” and why is this important when expressing proteins in other organisms? 41. The segment on the mechanics of translation will be presented as a Screenwatch™ Powerpoint / Podcast that you will view out of class on your own time. You are responsible for this information, as it was discussed in fairly great detail in BIO 151. 42. Describe the structure of a ribosome; include rRNA and ribosomal proteins. We will leave much of this gory detail for a biochemistry course. 43. Discuss the significance of the “enzyme activity” of rRNA and of “catalytic RNA” in general. 44. Describe a tRNA and discuss its importance. What are anticodons, and amino-acyl acceptor sites? 45. What are amino acyl tRNA synthetases? 46. Compare eukaryotic and prokaryotic ribosomes. 47. Describe the events of the initiation of translation. What re IF s? 48. Describe the events of translational elongation. What re EF s? 49. What is the source of energy for elongation? Be specific. 50. How and why does translational termination occur? What are RF s? 51. Name 3 antibiotics that affect translation describe how they work. 52. Define and describe point mutations; distinguish between silent, radical missence, conservative missence, and nonsense (chain termination) mutations (may have to go back to 151 to review). 53. Describe frame-shift mutations. 54. What were the major contributions made to genetics by Drs. George Beadle & Edward Tatum, Linus Pauling, Gobind Khorna & Marshall Nirenberg? 4
  5. 5. Techniques of Gene Cloning and Recombinant DNA: Chapters 19 1. Define recombinant DNA (rDNA) and discuss how it has revolutionized genetics and life sciences in general. 2. Describe the overall concept of the cloning procedure and discuss its significance. 3. Describe the synthesis of cDNA; include the steps and enzymes involved. Why is cDNA so important, especially when dealing with organisms with large C values? 4. What is a gene library. What is the correlation between C value of the organism represented in the library and the vector used in the cloning procedure 5. Describe, in detail, the features of pBR322 and pUC based plasmid vectors. 6. Describe the virtues of using phage as a cloning vector. 7. Briefly describe the virtues of using other vectors such as cosmids, YACs, BACs and animal or plant viruses. 8. What are restriction endonucleases and why are they important? 9. Describe the restriction modification systems in bacteria and discuss how they were genetically elucidated. 10. What is a palindrome? What is a sticky end, a blunt end, a 5’ overhang and a 3’ overhang? 11. Distinguish between 4-cutters, 6-cutters and 8-cutters; with what frequency would they be found in a genome? 12. What is the role DNA ligase in making rDNA? 13. Describe the process of transformation. 14. Outline the steps involved in creating rDNA in pBR322 plasmids; include the replica plating process. 15. Discuss how pUC vectors simply the screening process 16. What is a gene library and why are they important? 17. Describe how one goes about finding/screening a desired rDNA clone in a library. 18. Describe the role of the probe in library screening? 19. What are synthetic oligonucleotides and why are they useful? 20. What is cloning by complementation? What is its limitation? What is its virtue? 21. What is chromosomal walking? 22. Describe PCR and discuss its power and uses. 23. Discuss the importance of restriction mapping. 24. Describe the principles of the restriction mapping techniques. Be able to solve simple restriction mapping problems using either double digest or partial digest labeling technique. 25. Understand the theory, principles and practice of the Sanger Dideoxy sequencing method. 26. When and why would you use acrylamide gel electrophoresis instead of agarose gel electrophoresis? 27. List and discuss several uses of DNA sequencing data. 28. Why is it so much more productive to analyze protein function via the route of DNA sequencing rather than direct analysis of proteins. Explain. 29. Explain the steps in producing a Southern blot? Why is this technique so named? What are some uses of this technique? 30. What is an RFLP and what is its usefulness? 5
  6. 6. PART II Extensions of Mendelian Inheritance: Sex Chromosomes, Multiple Alleles, Epistasis, , etc. Chapters 7 & 4 1. Define sex linkage and discuss the patterns of inheritance observed with X-linked genes. 2. Explain the chromosome theory of inheritance. What was the contribution of Boveri? 3. Understand the different patterns of inheritance when comparing a sex-linked to an autosomal gene. 4. What determines sex in mammals, Drosophila and birds, etc.? Include the “heterogametic sex” and “homogametic sex.” Note we will not deal with genetics problems dealing with species with homogametic males (e.g. birds, moths, etc.) or autosome/sex chromosome ratios in Drosophila. 5. What is the role of X-inactivation in mammals and describe how it works. 6. Understand the range of dominance relationships that can occur between alleles of one gene, including instances when many different alleles exist for a specific gene (multiple alleles). 7. Distinguish between incomplete dominance, codominance, and overdominance. Give examples of each and be able to solve problems. 8. How are complementation and segregation tests used to determine if different mutations are alleles of the same gene or of different genes? 9. Distinguish between penetrance and expressivity. 10. What is a dominant lethal gene, and how does it differ from a recessive lethal gene in its inheritance pattern? 11. Distinguish between the various types of mutant alleles that may exist for a given gene; loss of function alleles (hypomorphic, amorphic, & null alleles) and gain of function alleles (hypermorphic, neomorphic and antimorphic). 12. How do the alleles in the preceding question relate to protoncogenes and tumor suppressor genes that are involved in cancer? 13. What are conditional mutations and why are they so valuable? 14. What is an auxotrophic mutant? 15. Understand how the expression of one gene can affect the inheritance of phenotype of another gene, including dominant and recessive epistasis, and modifier genes. 16. Be able to recognize dominant and recessive inheritance patterns in “modified” dihybrid crosses. 17. Answer all relevant problems and perform the genetic media lab activities at the end of the chapters (CD and or web site). Introduction to Quantitative / Polygenic Inheritance: Highlights of Chapter 24 1. Define polygenic inheritance / quantitative traits and give several examples. 2. Do quantitative traits violate Mendel’s rules? Explain. 3. What kinds of graphical depictions exemplify quantitative traits? 4. What are additive alleles? 5. Understand that analysis of quantitative inheritance is an exercise in Mendelism and statistics. Define and use correlation and regression, variance, and heritability. 6. Be able to solve “Chapter 5 Review Problems 7. Answer any relevant problems and perform the genetic media lab activities at the end of the chapter (CD and or web site). 6
  7. 7. Genetic Mapping Using Linkage Analysis: Chapter 5 1. What is genetic linkage and how is it determined? 2. How do you construct a genetic linkage map from the phenotypes of the progeny of a cross? 3. Be able to construct genetic maps using a series of data from dihybrid test crosses. 4. Understand how to calculate linkage map distances using three point test crosses, like the example given in class. 5. What is the advantage of a 3 point test cross vs. a 2 point cross in mapping? 6. What is the relationship between the frequency of crossing over and linkage map distance? 7. Define interference. 8. Understand how to construct linkage maps via unordered tetrad analysis, e.g. Saccharomyces cerevesiae. 9. Understand how to maps two genes relative to the centromere via ordered tetrad analysis utilizing two genes, as in Neurospora crassa. 10. Define mitotic recombination and discuss its importance. 11. Classically, how were genes assigned to chromosomes by cell fusion? Understand the basis of HAT selection. 12. What are polytene chromosomes and why are they so useful? 13. Answer all relevant problems and perform the genetic media lab activities at the end of the chapter (CD and or web site). Dissection of Gene Function by Forward and Reverse Genetics: Chapter 21 1. Note that this concept is theme of this course and is integrated throughout. 2. Explain how deficiency complementation mapping works and be able to solve problems such as the example discussed in class. 3. Define intragenic complementation and understand how fine structure genetic analysis maps functional regions within a gene. 4. Define cistron and complementation group. Who coined the term cistron? 5. Discuss how complementation testing may be used to genetically dissect complex processes; be able to work with a complementation matrix. 7
  8. 8. Introduction to Bacterial and Viral Genetics: Chapter 6 1. Why are bacteria so useful to genetics and why were they not used in the early years of genetics (1900-1940)? 2. Who was Joshua Lederberg and what was his contribution to genetics? 3. Define and discuss the virtues of auxotrophic mutants and temperature sensitive mutants, AGAIN. 4. Describe F factor plasmids and their role in conjugation. 5. What are Hfr strains and why are they useful? 6. Describe how bacterial genes are mapped and be able to solve simple problems like the one presented in class. 7. How does the genetic map of bacteria differ from that in eukaryotes? 8. What are F’ plasmids and “partial diploids?” 9. Describe transformation and discuss its modern uses. 10. Describe the structure and biology of viruses. 11. Describe the lytic and lysogenic life cycles of bacteriophage. 12. Define transduction; how does it relate virally induced carcinogenesis? 13. Describe how genetic crosses in done in phage and be able to solve a problem like that presented in class. 14. Answer any relevant problems and perform the genetic media lab activities at the end of the chapter (CD and or web site). Introduction to Mitochondrial and Chloroplast Genetics & Genomes: Chapter 9 1. Review and understand the features of the endosymbiont theory of the origin of eukaryotic cells. Who proposed it and what evidence supports it? 2. What is maternal inheritance and why does it occur? 3. Why is mitochondrial DNA so valuable to evolutionary and migration studies? 4. Distinguish between homoplasmic and heteroplasmic. 5. Describe the features of mitochondrial genomes. How big are they and why are there so few genes? 6. Describe the features of chloroplast genomes. How big are they and why are there so few genes? 7. Answer all relevant problems and perform the genetic media lab activities at the end of the chapter (CD and or web site). Chromosomes & Chromosome Mutations: Chapters 12 & 8 1. Describe the structure of prokaryotic chromosomes and the possible role of the HU proteins. 2. Describe supercoiling and how it is described by topoisomerase I and II. What is linking number? 3. Define and discuss the “C-value paradox.” 4. Describe the arrangement of eukaryotic DNA into functional genes and “junk” repetitive DNA. 5. Define and distinguish between LINES, SINES and Satellite DNA. 6. Discuss the concept of a transposon. Which repetitive DNA families may be transposons? 7. Read and understand the paper on “Genomic Scrap Yards” (Gene, 259, 61-67, 2001) 8. Describe the structure of a nucleosome. 9. Why are histones composed of basic amino acids? Explain. 10. Describe the higher order structures chromosomes may assume, e.g. solenoids and 300 nm loops. 11. Discuss chromatin dynamics as it relates to the above and to gene expression; distinguish between euchromatin, constituitive heterochromatin and facultative heterochromatin. 12. Describe FISH. What technique has FISH pretty much replaced? 8
  9. 9. 13. Describe how methylation may be correlated with gene expression and chromatin structure. 14. What are the functions, composition and structure of centromeres, as genetically defined in yeast? 15. Describe the function and composition of telomeres. 16. Discuss the “3’ end problem” confronted by telomeres and discuss how telomerase maintains these structures. How does telomerase relate to aging and malignancy? 17. Define, describe and comment on the possible causes and consequences of the main types of gross chromosomal mutations: inversions, translocations, deletions and duplications. 18. What happens during non-disjunction of meiosis that causes the improper segregation of chromosomes? 19. Define aneuploidy and discuss how it arises; include nullisomy, monosomy, and trisomy; also discuss the importance of nondisjunction. DNA Mutation, Repair & an Introduction to Cancer Genetics: Chapters 15 & 18 1. Describe the result from DNA replication errors. How do cells minimize these errors? 2. Define, describe and state the consequences of neutral / silent, missence (radical and conservative), nonsense and frameshift mutations. 3. What are transitions and transversions? 4. Explain how UV light affects DNA and how cells respond to UV damage. 5. Understand how nitrous acid, hydroxylamine, alkylating agents, and intercalating agents affect DNA. 6. Describe the Ames test and discuss its importance. 7. Describe DNA repair mechanisms, such as excision repair, DNA glycosylase/AP endonuclease, and recombination repair mechanisms. 8. What are insertion sequences and transposons? Who discovered transposons? 9. What are the main types of transposons and retroposons? 10. Distinguish between an oncogene and proto-oncogene. How were oncogenes discovered? 11. What are the main types of proto-oncogenes? Give examples about how they are mutated to become oncogenes. 12. What is a tumor-suppressor gene or antioncogene. Give examples. What is P53 and briefly describe its function. 13. Describe the multi-step theory of tumor formation and discuss how this relates to polygenic inheritance and environmental factors. 9
  10. 10. PART III Applications of rDNA: Genomics, Transgenics, Gene Therapy, etc. Chapters 19 & 20 1. What is genomics and why is modern genetics considered to be in the genomics age? 2. Discuss why having DNA sequence data is not an “end all” and why traditional genetics is still so crucially important. 3. Describe some 4. Describe how you could detect an RFLP that created a new restriction enzyme site in an exon of a known gene, e.g. Src, that is involved in cancer. 5. Describe the principle of DNA fingerprinting. 6. Describe the theory, method and results of the PCR based DNA fingerprinting technique that you did in lab. What locus (loci) was the target? 7. What is a northern blot? How does it differ from a Southern blot, in theory and practice? 8. Analyze the results of the following northern blots: A. If you had a probe for gene X and it revealed a 1.4 kb band in all tissues, what could you conclude? B. If you had a probe for gene Y and it revealed a 1.1 kb band in nerve tissue only, what could you conclude? C. If you had a probe for gene Z and it revealed a 1.0 kb band in the cytoplasm of adult nerve tissue, but a 1.9 kb band in nuclear RNA, what could you conclude? D. If you had a probe for gene A and it revealed a 1.0 kb band in skin, 1.4 kb band in intestinal cells and a 1.2 kb band in the ovary, what might you be able to conclude? How could you test your hypothesis? 9. Describe the basic principle behind a microarray and discuss its applications. 10. What are transgenic organisms and why are they so useful? 11. What are the requirements for expressing of a eukaryotic gene in a prokaryotic system. Describe the requirements of the cloning vector. 12. Describe the Agrobacterium tumefaciens / Ti plasmid system for production of transgenic plants. 13. What are P elements and how are they used? 14. Describe the process of producing transgenic mammals, in detail. 15. Describe how you can use transgenic mouse technology to investigate tissue specific gene regulation. 16. What is a “reporter gene” and how is it used? 17. Define “reverse genetics” and discuss why it is so important in the “modern genetics” or recently evolved mammals, e.g. mice. 18. Describe, in detail, the process of producing a null phenotype (gene knockouts) using ES cells, gene targeting, etc. What are the features of the vector? How do “gene knock in” approaches work? 19. Describe the principle of gene therapy and distinguish between augmentation and replacement. Why are researchers having so many problems with gene therapy? 20. What were the major contributions made to genetics Hamilton Smith/Daniel Nathans & Werner Arber, Herbert Boyer & Stanley Cohen and Kerry Mullis? Regulation of Gene Expression in Prokaryotes: Chapter 14 1. Define transcriptional control, posttranscriptional control, translational control and posttranslational control. Contrast these issues in prokaryotes and eukaryotes. 2. Describe the role of the promoter, and associated regions, in transcriptional control. Discuss the current understanding of the mechanism promoter function. 3. Define transcription rate and discuss its regulation. 4. Define and compare constitutive gene expression and regulated gene expression. 10
  11. 11. 5. Define and describe the concept of the prokaryotic operon. 6. Describe the structure of the lactose operon; include the repressor, operator and the structural (coding) genes. Know all symbols and genetic designations. 7. Explain, in detail, how Jacob and Monod utilized mutant strains and F’ plasmids, to decipher lac operon function, include polar mutants, repressor mutants, operator mutants, and superrepressor mutants. 8. Genetically speaking, what does working in cis or in trans mean? 9. What is meant by the idea that the lac operon is inducible? 10. Describe repression and induction of the lac operon. 11. Discuss the role of the CRP protein in greatly increasing lac operon transcription. What is cAMP? 12. Describe the concept of a repressible operon, e.g. the tryptophan operon, compared to an inducible operon. 13. Describe the function of the TRP repressor and explain how it works. 14. Define attenuation and describe this process in the TRP operon. Could attenuation, as described here, function in eukaryotes? Why? 15. What were the major contributions made to genetics by Francois Jacob & Jacques Monod and Charles Yanofsky? Regulation of Gene Expression in Eukaryotes: Chapter 14 & parts of 15 & 16 1. With respect to eukaryotic genes, discuss some generalizations that can be made about how they are regulated, when compared with prokaryotic genes. 2. Review and know how chromatin structure reflects gene expression; include euchromatin, facultative heterochromatin, constitutive heterochromatin, polytene chromosomes, nucleosome structure, methylation. 3. What is a housekeeping gene? 4. Define differential gene expression. 5. Describe how the Gal1 gene is regulated by GAL4, GAL80 and galactose. 6. What is the “heat shock” phenomenon and how are HS genes activated? 7. How do steroid hormones activate gene expression? 8. What re the three classes of genes that control development in Drosophila, and, in all likelihood, all animals. 9. Distinguish between gap, pair rule and segment polarity genes in the segmentation class of developmental genes. 10. What is a homeotic gene and what is a homeobox? 11. Describe Antennapedia. 12. What is meant when it is said the developmental genes “work in a hierarchy?” Review and know how geneticists utilize mutagenesis, complementation matrices, etc. to “dissect” complex developmental processes. 13. Describe the process of alternative RNA processing and discuss its importance. 14. With respect to introns and exons, comment on gene/genomic evolution. 15. Discuss RNA editing. Why is this so bizarre? In what organism was it first discovered? Does it also occur in humans? What is an editosome and what are “guide RNAs.” 16. Discuss the importance of differential mRNA stability and variable half-lives of mRNA. Explain the destabilizing phenomenon observed in the c-fos and c-myc proto-oncogenes. 17. What is translational control and what are masked maternal mRNAs? Where are these mRNA molecules typically found? Why? 18. What were the major contributions made to genetics by Philip Sharp, Tom Cech, Christine Nusslein- Volhard, Erich Weischaus and Ed Lewis? 11
  12. 12. Population Genetics Chapter 25 1. Describe allelic variation in populations. What molecular techniques are used to detect allelic variation? 2. What are allele frequencies and how are they calculated? 3. Understand the Hardy-Weinberg equation and be able to use it to determine allele and genotypic frequencies. 4. Under what conditions is HW equilibrium achieved? 5. Explain how the 2 test can be used to determine if a population is in HW equilibrium. 6. How do non-random mating, mutation, migration, selection and genetic drift affect allele frequencies in a population. Time will determine how much we get into the math! 7. Define speciation and understand how it is thought to occur. Molecular Evolution: Chapter 26 1. This topic will be discussed as time permits; bit and pieces of this may be integrated in with the above topics. 2. What is a gene family and how are they though to have arisen? 3. What is a pseudogene? 4. Explain how introns may have arisen; distinguish between the two theories. 5. Explain why nucleotide substitutions occur at different rates in different parts of a gene. 6. What is a molecular clock and how is this information used to create phylogenetic trees? 7. Why is mitochondrial DNA such a nice molecular clock? Term Paper: 1. Survey the literature and write a term paper on a genetics topic, as outlined in the instructions. 12

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