Exam 4 ID#: July 7, 2008

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1 Biology 4361 Name: KEY Exam 4 ID#: July 7, 2008 Multiple choice (one point each; indicate the best answer) 1. RNA polymerase II is not able to transcribe RNA unless a. it is first bound to TFIIB. b. its carboxy-terminal domain is phosphorylated by TFIIH. c. it changes configuration and is released from TFIID. 2. Many TAFs act by a. increasing DNA methylation. b. increasing histone methylation. c. increasing histone acetylation. d. decreasing histone acetylation. 3. Enhancers differ from promoters in that they a. are made of protein. b. must operate in close proximity with the transcription start site. c. can bind transcription factors. d. can operate in a reverse orientation. 4. If you modify an FGF-α gene to contain a β-galactosidase reporter and insert it into a developing mouse embryo, you should detect a blue signal a. wherever FGF-α is expressed. b. wherever FGF-α binds to a receptor. c. both of the above. d. neither of the above. 5. Zinc finger, basic helix-loop-helix, and homeodomain are a. transcription factor families. b. genes involved with early development. c. tertiary protein structures. d. basal transcription factors 6. TFIID, TFIIB, and TFIIA a. bind to the core promoter. b. form a portion of the transcription initiation complex. c. bind RNA polymerase II. 7. DNA methylation controls transcription in a. Drosophila. b. vertebrates. c. invertebrates. 1

2 8. In vertebrates, the lens is induced by a. neural ectoderm. b. forebrain tissue. c. the optic vesicle. 9. An optic vesicle transplanted to the vicinity of the posterior epidermis in the same embryo failed to induce a lens in that tissue. The most probable explanation for this result is that a. the vesicle lost its inductive ability. b. the posterior epidermis lacked competence. c. another inductive signal blocked the lens induction. d. the posterior epidermis was already terminally differentiated. 10. Instructive inducing signals a. tends to restrict a cell s possible fates. b. tend to increase the possible breadth of a cell s possible fates. c. tends to regulate the degree to which a specified tissue might respond. d. generally do not result in new gene expression. 11. A signaling molecule that is produced by one cell and has its effect in another cell after traveling through the intracellular space is called a a. juxtacrine factor. b. paracrine factor. c. autocrine factor. d. endocrine factor. 12. Epithelium and mesenchyme a. can convert into one-another. b. are unchangeable, once established. c. usually are unrelated cell types. d. none of the above. 13. An intercellular signal that requires the contact of two cells for transmittal is called a a. juxtacrine factor. b. paracrine factor. c. autocrine factor. d. endocrine factor. 14. In the Notch signal transduction pathway, the receptor a. remains on the signaling cell. b. diffuses between the two cells. c. undergoes proteolysis. d. none of the above. 15. A group of cells may stabilize their differentiation state by exchanging signals. This is termed the a. autocrine effect. b. community effect. c. stabilization effect. d. none of the above 2

3 16. Sea urchin cortical granule serine protease a. cleaves protein connections between the plasma membrane and vitellin envelope. b. clips off ZP3 components and releases connected sperm. c. cleaves and inactivates acrosomal proteases. 17. Mammalian eggs are usually surrounded by a. cumulus cells. b. the corona radiata. c. follicular cells d. all of the above 18. Resact is a. produced by sea urchin sperm. b. a chemoattractant. c. a guanylyl cyclase enzyme. d. all of the above 19. Sea urchin gametes form connections through a. egg actin. b. sperm actin. c. cytoplasmic bridges. 20. Which of the following would NOT be expected to change during sperm capacitation? a. membrane potential b. membrane components c. protein phosphorylation d. flagellar length 21. What molecular component of the mouse zona pellucida binds to sperm cells? a. N-acetylglucosamine b. galactosyltransferase c. bindin d. serine protease 22. The mouse sperm acrosome reaction involves a. membrane fusion. b. Ca 2+ concentration changes. c. G-protein activation d. all of the above 23. Egg cytoplasm extends around the sperm head and draws the sperm inside in a. sea urchin fertilization. b. mammalian fertilization. c. both types of fertilization. d. neither type of fertilization. 3

4 24. The SED1 protein is involved in a. inducing sea urchin sperm-egg binding. b. inducing mouse sperm acrosome reactions. c. mouse sperm-egg binding. d. mouse zona pellucida hardening. 25. In sea urchins, the spicules will arise from a. bone fragments. b. skeletogenic mesoderm. c. aboral ectoderm. d. vegetal plate endoderm. 26. The first phase of sea urchin gastrulation is a. vegetal plate ingression. b. vegetal plate invagination. c. primary mesenchyme cell ingression. d. primary mesenchyme cell invagination. True / False (1 point each) 27. Dosage compensation refers to techniques that adjust the level of antibiotic resistance genes in knockout experiments. True / False 28. Nuclear hormone receptors are a sub-family of transcription factors. True / False 29. Enhancers always increase transcription rates. True / False 30. In sea urchin sperm a decrease in internal Ca 2+ plays a part in triggering the acrosome reaction. True / False 31. If an inducing signal directs the degree to which a specified tissue responds, it is likely to be a permissive signal. True / False 32. Many tissues require multiple inductions. True / False 33. Apoptosis is always initiated by paracrine signals. True / False 34. Cells can maintain their own differentiation by permanently modifying their DNA structure to prevent nucleosomes from forming. True / False 35. In mammals it is impossible for immotile sperm to get to the oviduct. True / False 36. Sea urchin sperm bind to the egg vitelline envelope via bindin proteins. True / False 37. Mammalian sperm capacitation requires gene transcription. True / False 38. In mammalian sperm it would be reasonable to expect that egg recognition proteins would be found only at the tip of the nuclear envelope. True / False 4

5 39. Male pronuclear rotation positions the centriole in the proper position to draw the male and female pronuclei together. True / False Define. Write a brief definition of any six of the following terms or phrases (2 points each): 40. Basal transcription factors Small, constitutive, ubiquitous nuclear proteins that are necessary components of the transcription preinitiation complex; generally assist in RNA polymerase II binding. 41. Capacitation A series of physiological maturational changes that mammalian sperm undergo in the female reproductive tract; necessary for sperm fertility. 42. Cis-acting regulators of transcription DNA sequences (enhancers) that bind proteins (transcription factors) which regulate transcription by affecting basal transcription factors or RNA polymerase II at the promoter. 43. Egg activation Physiological events within the egg that take place after fertilization (or suitable stimulation); include fast and slow blocks to polyspermy, metabolic activation, resumption of the cell cycle. 44. Genetic specificity of induction Mesenchymal tissue induced overlying ectoderm, but the range of possible responses will be constrained by the content of the ectodermal genome. 45. Reciprocal induction A phenomenon whereby two cells or tissues act as inducing and responding tissues for each other. 46. Self-propagating calcium wave A phenomenon where an initial release of calcium ions (from, for example, endoplasmic reticulum) stimulates calcium release from adjacent compartments, which stimulates further release, etc. 47. Signal transduction The process by which an extracellular signal is received at the membrane (or in the cytoplasm), where it initiates changes in cytoplasmic proteins that eventually result in the activation or inhibition of gene transcription. 48. Transcription factor domains Specific areas of the proteins that allow, e.g. dimerization with other proteins, DNA binding, and transcriptional activation. 5

6 Short Answer. Answer any four (6 points each). Be certain to address all parts of the questions. 49. Describe four mechanisms that differentiated cells might use signal transduction pathways or control of gene transcription to maintain their differentiated state. 1) Activating signal initiates production of a transcription factor which stimulates transcription of its own gene. 2) Synthesized proteins act to stabilize chromatin to keep gene accessible. 3) Autocrine signaling: same cell makes signaling molecule and receptor. 4) Paracrine loop - interaction with neighboring cells such that each stimulates differentiation of the other. 50. Explain the statement Enhancers are modular and combinatorial. Enhancers are short DNA sequences that can be inserted into the regulatory regions of a variety of genes as independent modules. Enhancer modules can be used in numerous combinations to regulate different genes. 51. Briefly define each of the following and describe the general relationships between them: basal transcription factors, TAFs, and specific transcription factors. Basal transcription factors are a set of small, constitutive, and ubiquitous nuclear proteins that sequentially bind to the promoter and allow RNA Polymerase II binding to the DNA. TAFs (TBP Associated Factors) are small nuclear proteins that bind to or associate with the TATA Binding Protein (TBP) subunit of TFIID. Specific transcription factors are proteins that bind to and activate enhancers. TAFs bind to basal transcription factors and to specific transcription factors, as well. They often function to destabilize histone/dna interactions, increasing transcriptional activity. 52. Certain promoters are referred to as weak promoters ; they generally do not support rapid or sustained transcription. List two possible reasons why promoters might be weak, and describe how those characteristics could act slow transcriptional rates. 1) Low affinity binding of general transcription factors/rna PolII - transcription factors would not remain bound to the promoter for long periods 2) Tight association with nucleosomes - prevents general transcription factor binding 6

7 53. Describe the fast block to polyspermy in sea urchin eggs. Sperm binding (or fusion with egg membrane) causes Na + influx into egg cell; membrane potential shifts from resting ~-70 mv to ~20 mv; sperm cannot bind to membrane with a positive potential 54. There are four major components in cortical granules. List them and describe the specific function of each. Serine protease: dissolves protein connections between vitelline envelope and egg membrane; clips bindin receptors and releases remaining sperm Mucopolysaccharides: hygroscopic- elevate the fertilization envelope as they hydrate Peroxicases: crosslink tyrosines in intervitelline space; harden fertilization envelope Hyaline: forms a protective coating around the egg 7

8 Short Essay. Everybody should answer Question 55 (15 points). Then answer either 56 or 57 (10 points each). Be certain to address all parts of the questions and provide complete answers. 55. A) Draw the receptor tyrosine kinase signal transduction pathway. Label and describe the essential molecular components, activation points, and recycling steps. Be sure to include the location of all of the components (e.g. extracellular, cytoplasmic, etc.). B) Define proto-oncogene; specify which components of the RTK pathway have been identified as proto-oncogenes, and explain why mutations of proto-oncogenes are commonly associated with tumor formation. C) There are several places in the RTK pathway that might be used by cells to control the initiation or speed of the pathway. Identify be two of these points and explain how they might be used to control pathway activity. B) Proto-oncogene genes that, if inappropriately activated, can trigger cancers. Ras, Raf, Mek, Erk are considered proto-oncogenes C) Ligand-receptor binding low concentration of ligand; weak binding Ras low concentration of GDP; low concentration of GAP protein Low concentration of any of the intermediate activating proteins Transcription factor low concentration Gene methylation/tight association with nucleosomes 8

9 56. Define the basic components of the morphogen gradient and polar coordinate models of regeneration. For each model, explain how a new (regenerating) cell or tissue might be specified. Morphogen gradient existing and regenerating cells obtain positional information by sensing a growth-promoting morphogen, which is produced at a discrete location (source) and diffuses towards a sink, forming a concentration gradient. A regenerating cell might react to the morphogen at different concentrations by stimulating different sets of signal transduction pathways, promoting multiple signal transduction pathways,or increasing or decreasing the flux of various pathways. Each of which could lead to differential gene activation and specification. Polar coordinate existing cells identify their positions in relation to neighboring cells, using cell surface markers to denote their position in both anterior-posterior and circumferential dimensions. During regeneration the unspecified cells use the cell surface markers on the existing adjacent cells to specify (i.e. stimulating differential gene expression, as noted above) such that they fill in the portions of tissues that are missing in shortest and most efficient way possible. 57. You transplant dermal mesenchyme tissue from the wing of a chick embryo to an area underneath the thigh epidermal epithelium of a lizard embryo of similar age. A) Describe the type of epithelium that you expect to be produced, and explain what principles of induction would be demonstrated. Lizard thigh epithelium (i.e. with scales) would be produced. - chick wing (i.e. limb) mesenchyme would send inductive tissues to the existing lizard epithelium, which would be constrained by the genetic specificity of induction to form lizard-type tissue B) Describe a control experiment that you could run that would confirm that your results were due specifically to the transplant. Perform the experiment using chick mesenchyme from a non-limb area. 9