BILD7: Problem Set. 2. What did Chargaff discover and why was this important?

Transcription

1 BILD7: Problem Set 1. What is the general structure of DNA? 2. What did Chargaff discover and why was this important? 3. What was the major contribution of Rosalind Franklin? 4. How did solving the structure of DNA immediately suggest (1) how genetic information is copied every time a cell divides and (2) how genetic information in DNA is stored? 5. What was the major conclusion from the Gurdon experiment? 6. The central dogma of molecular biology says that DNA makes RNA makes protein. What exactly does this mean? 7. What happens during transcription? 8. What is the difference between RNA and DNA? (hint: what are the structural differences between RNA and DNA, where is RNA made? Where does RNA function?). 9. What happens during translation and where in the cell does it occur? 10. During translation, is the genetic code read one, two, or three bases at a time and why? 11. Briefly describe an experiment, using DNA and bacteria, that demonstrates that DNA carries the genetic material. 12. Genes can generally be described as having two distinct parts. What are they? 13. Why is the sequence of amino acids that makes up a protein important? 14. What determines ( codes for ) the sequence of amino acids in a protein? 15. What is a mutation? How can it cause a protein to lose its normal function? 16. What is meant by the statement the genetic code is universal? 17. What is Gregor Mendel best known for?

2 18. What is the difference between genotype and phenotype? 19. Define the following: allele, homozygous, heterozygous, dominant, recessive. 20. Assume that + is a dominant functional allele required to make pea seeds round, and w is a recessive allele that makes pea seeds wrinkled. What are the ratios of the genotypes and the phenotypes of the F1 progeny from the following crosses: (A) +/+ X w/w (B) +/w X w/w (C) +/w X +/w (D) w/w X w/w 21. You are given a vial of red-eyed flies in which all of the flies look normal (that is, they have no visible abnormalities). You are told that these flies are carriers for a mutation (white) that causes eyes to appear white. What GENETIC experiment could you do to prove that they are indeed carriers of the white mutation? 22. What are the two major parts of a typical gene? 23. Explain what is meant by the term mis-expression of a gene. What can a researcher learn from mis-expressing a gene? 24. What is a transcription factor and what does it do? 25. In general terms, how do cells communicate with one another? (hint: e.g. via signals and receptors) 26. What is the difference in effect between a signal that is secreted versus one that is tethered to the cell? 27. What is a morphogen and how do such factors contribute to pattern formation during development? 28. Describe the Mangold-Spemann experiment. What important concept did this experiment reveal? 29. What morphogen initiates patterning along the nose-to-tail (anterior-posterior) axis of the fruit fly embryo? 30. What does it mean for a gene to be purely maternally acting (e.g., the bicoid gene) versus zygotically acting (e.g., the even-skipped gene)

3 31. When Christiane Nüsslein-Volhard, Eric Wieschaus, and Gerd Jürgens conducted their famous genetic screen for mutants affecting the formation of the embryonic body plan of fruit flies they found the following three classes of mutants: gap mutants, pair-rule mutants, and segment polarity mutants. What are the types of defects found for each of these classes of mutants and based on these defects, what type of hierarchical relationship between these genes did these researchers propose normally existed? 32. On what basis did Nüsslein-Volhard, Wieschaus, and Jürgens conclude that they had identified nearly all the genes that are required to pattern the cuticle? (hint: consider how many mutations they found and how many different genes these mutations disrupted) 33. In general terms, how is a pair-rule gene such as even-skipped turned on in a series of seven stripes in the fruit fly embryo? (e.g., think of how even-skipped is activated in stripe-3). 34. In the case of even-skipped stripe 3, what is the regulatory code for turning this genetic control switch on? 35. What is the name of the morphogen that initiates patterning along the belly-toback (dorsal-ventral) axis of the fruit fly embryo? 36. Name two genes activated in ventral regions of the embryo by high levels of Dorsal. What do each of these two genes do to promote mesoderm development? 37. What is the key gene that promotes development of the dorsal epidermis (skin) in fruit flies? 38. What is the default state of ectodermal cells in the early fruit fly embryo? 39. Name two genes required for formation of the lateral neuroectoderm in the fruit fly embryo. 40. What is the function of the short gastrulation (sog) gene in the neuroectoderm and how is this related to the default state of ectodermal cells? 41. What is the function of the brinker (brk) gene? How does this function compare to that of sog? 42. What is the function of Sog in patterning the dorsal non-neural ectoderm? What role does the tolloid (tld) gene play in this aspect of Sog activity?

4 43. What happens when sog messenger RNA (mrna) is injected into ventral mesodermal cells in frog embryos? Indicate what cell types formed from cells that were actually injected with the mrna versus the cell types that were generated by surrounding cells. 44. What is the function of the neural identity genes vnd, ind, and msh? What types of proteins do these genes encode? 45. What is meant by ventral dominant repression among neural identity genes? 46. How does Dpp signaling influence the expression of neural identity genes? How is this function of Dpp used to help create the relative pattern of msh and ind expression? 47. Besides Dpp signaling, what morphogen regulates expression of neural identity genes? Which neural identity gene is most dependent on this molecule for being activated? 48. What external event determines the location of the ventral pole of the frog embryo? 49. What maternal morphogen in frogs plays a critical role in establishing the dorsalventral axis? At which pole is this factor most concentrated? 50. What tissue types do the vegetal and animal hemispheres of the frog give rise to? Indicate the relative positions of these three tissue types on a drawing of a frog blastoderm stage embryo. 51. Where is Veg-T expressed in the early frog embryo? How does Veg-T lead to mesoderm induction in neighboring cells? 52. What two patterning mechanisms collaborate to induce expression of genes (e.g., chordin) in the Spemann Organizer of the frog embryo? 53. How is the anterior-posterior axis of the frog embryo oriented with respect to the ectoderm? 54. How is the anterior-posterior axis of the frog embryo oriented with respect to the mesoderm? 55. What genes are involved in determining segment identity in vertebrates? What are the fly counterparts of these genes called?

5 56. How are segment identity genes expressed in flies and vertebrates? 57. What are two properties of segment identity genes that can be used to equate a particular gene in flies with its counterpart in vertebrates? 58. What happens when the fly Antennapedia gene is misexpressed in the head of a fly? Why does this happen? 59. What happened when Bill McGinnis misexpressed the mouse counterpart of Antennapedia (Hox 6) in the fly head? What important conclusion did he and his colleagues come to based on the results of these experiments? 60. How does the dorsal-ventral axis of a vertebrate embryo compare with that of an invertebrate like the fly? 61. To what fly genes do the vertebrate BMP-4 and chordin genes correspond? 62. How are the BMP-4 and chordin genes expressed in the frog embryo? (e.g. in what cell types and regions) 63. What happens when chordin RNA is injected into ventral mesodermal cells of a frog embryo? Ditto for injection of fly sog RNA? How does this compare to the result of the Mangold-Spemann experiments? 64. In the years following the Mangold-Spemann experiments, why did the scientific community conclude that the default state of ectoderm was epidermal? What was an experiment which ran counter to this prevailing view and why was it discounted? 65. Describe a recent experiment that reconciles the classic embryological experiments with the modern molecular view of neural induction? What is the default state of ectoderm in both vertebrates and invertebrates? 66. How are the vertebrate counterparts of the Drosophila neural identity genes (Msx1, Gsh, and Nkx2.2.) expressed in the neural tube? What two signaling systems play a role in creating this pattern of neural identity expression in vertebrates? Which of these systems also function to pattern the fly nervous system and which system is only used to pattern the vertebrate nervous system? 67. What are the three basic axes of an appendage such as wing or leg? Identify regions of your arm and hand that would illustrate these forms of polarity.

6 68. When are imaginal discs first generated during development in insects such as fruit flies that undergo metamorphosis? 69. In general terms, how is the adult put together from imaginal discs during metamorphosis? 70. What happens to most of the cells that are not part of an imaginal disc in a fly pupa undergoing metamorphosis? 71. At what developmental stage is the wing primordium in a fruit fly first partitioned into anterior and posterior halves? 72. Describe in general terms how the anterior-posterior axis is established in a developing wing imaginal disc (e.g. how do Engrailed, Hedgehog, and Dpp function? Which ligand exerts a short range action and which ligand acts at long range?) 73. What is a simple general mechanism for making lines during development? Explain how this mechanism accounts for the pattern of dpp expression in the middle of the wing disc and for placement of the L2 vein just anterior to the broad central domain of spalt expression. 74. What is the name of the structure that forms at the interface of the dorsal and ventral halves of the wing primordium? What morphological features of this structure distinguish its dorsal from ventral parts? 75. What happens if an experimenter removes the function of the gene apterous, which determines dorsal cell identities in the wing, from a small patch of cells on the dorsal surface? What does the result of this experiment tell you about normal wing development? 76. For what process is the distalless gene required? 77. What two conditions must be met to activate expression of distalless in a fly leg? (e.g. how is it that distalless is expressed just at the tip of the growing leg?) 78. What defect is observed in flies lacking function of the eyeless gene? What happens if eyeless mis-expressed in the developing wing? 79. What is the vertebrate ZPA and how was it identified? What morphogen is produced by the ZPA and what line of experimental evidence demonstrates that different levels of this factor elicit distinct developmental responses?

7 80. Discuss the parallels between flies and vertebrates in patterning the A/P, D/V and P/D axes of appendages? Given these similarities is it reasonable to conclude that vertebrate and invertebrate appendages derived from an outgrowth in the body wall of a common ancestor? Is there reason to believe that chicken wings derived from fly wings? 81. What are some of the similarities between vertebrate and invertebrate eye development? Do eyes in these two types of animals appear similar? In what respect does the fly eye outperform the vertebrate eye, and conversely, what is an advantage of vertebrate vision? 82. Why has it been proposed that eyeless/pax6 function as eye master genes? What are two arguments against this idea? 83. Name some of the characteristics of the most recent common ancestor of flies and humans. What kinds of evidence allow us to reconstruct these features? 84. What are some possible reasons to explain the fact that all segmented animals arose from a complex common ancestor with a well organized body plan and specialized cell types (e.g. what happened to all of the other animal forms that must have lived as the same time as our ancestor?) 85. Cell migration during gastrulation plays a major role during animal development. Describe a major difference between plant and animal cells that prevents plant cells from migrating. 86. What are the two basic strategies that plants use to grow in one direction versus another? 87. What roles do the plant hormones gibberellic acid (GA) and ethylene gas play during plant cell growth? 88. Draw a diagram of a heart-shaped embryo and label the morphologically distinct parts. 89. The L1, or epidermal cell layer is clonally distinct, meaning that when L1 cells divide they always remain in the L1 layer. How is this achieved? 90. What is the general phenotype when the WUSCHEL gene is inactivated by mutation? What happens when the CLAVATA3 gene is inactivated by mutation? What happens in double mutants in which both the WUSCHEL and CLAVATA3 genes are both inactivated?

8 91. Draw a diagram of a shoot meristem. Show the approximate locations where the WUSCHEL, CLAVATA1 and CLAVATA3 genes are expressed. Describe the general mechanism that plants use to maintain the stem cell population throughout the life of a plant. 92. Flower meristems arise on the flanks of the shoot apical meristem. What are two genes that specify flower meristem identity? What happens when these two genes are inactivated by mutations? 93. A shoot meristem is indeterminate and can continuously produce flower meristems on its flanks. However, when the TERMINAL FLOWER gene is inactivated by mutation, the indeterminate shoot meristem is used up in the production of a terminal flower. What is the normal function of the TERMINAL FLOWER gene and what happens to the expression pattern of the flower meristem identity genes when the TERMINAL FLOWER gene is inactivated by mutation? 94. Diagram the ABC model of flower organ identity and describe its basic principles. What are the phenotypes of A, B, and C single mutants, BC double mutants, and ABC mutants triple mutants? 95. The A-function gene (which is called AP1 in Arabidopsis) is initially expressed in all cells of the flower meristem but later becomes restricted to the two outer whorls (1 and 2) where it contributes to sepal and petal identity. How is AP1 RNA excluded from the two inner whorls (3 and 4)? 96. The C-function gene (which is called AGAMOUS in Arabidopsis) is expressed only in the center of flower meristems (whorls 3 and 4). What two genes participate in the activation of AGAMOUS? 97. What happens if the AGAMOUS gene is ectopically expressed in first whorl organs? 98. The B-function genes are expressed in whorls 2 and 3 where petals and stamens will form. What gene ensures that the B-function genes are not expressed in the fourth whorl? If this gene is inactivated by mutation, causing the B-function genes to be expressed in the fourth whorl, what is the resulting phenotype? 99. Flowers are determinate structures in that they produce four whorls of organs and then stop. However, when the C-function gene (AGAMOUS) is inactivated by mutation, these flowers become indeterminate and continuously produce additional organs. Why does this happen?

9 100. Diagram a wildtype Arabidopsis fruit and show the positions of the stigma, style, ovary, seeds, valves, replum and valve margin (dehiscence zone). Also show a diagram of a cross section through the ovary and note the positions of the valves, replum and valve margin (dehiscence zone) What is the phenotype(s) of FRUITFULL mutants? Where is the FRUITFULL gene normally expressed. What genes become ectopically expressed in FRUITFULL mutants? What happens to replum and valve margin cells if the FRUITFULL gene is ectopically expressed in all cells of the fruit? 102. What happens when the SHATTERPROOF or INDEHISCENT genes are inactivated by mutation? 103. What happens when the three genes FRUITFULL, SHATTERPROOF and INDEHISCENT are inactivated by mutation? What does this triple mutant reveal about the genes that cause the FRUITFULL mutant phenotype? 104. What happens to the replum when the REPLUMLESS gene is inactivated by mutation? What genes are ectopically expressed in the replum in the REPLUMLESS mutant? How do we know that the SHATTERPROOF genes are at least partly responsible for the loss of replum formation in the REPLUMLESS mutant? 105. What two processes does the PHANTASTICA gene control during leaf development? Compare the defects observed in PHANTASTICA mutant leaves with those observed in fly wings lacking the function of the apterous gene, which creates an organizing center at the interface between the dorsal and ventral domains of the wing primordium Auxin and cytokinin are two important plant hormones. Describe how the relative levels of these two hormones can promote shoot, root, or unorganized cell growth. Describe the steps involved in regenerating an intact plant from a single plant cell Name three genetic engineering technologies applied to plants or animals that are likely to shape the future. Describe these technologies with a single sentence for each.