Biology 4361 Name: KEY Exam 1 ID#: June 29, 2009 Multiple choice (one point each; indicate the best answer) 1. According to von Baer s laws, developing embryos a. pass through the adult stages of lower animals. b. pass through the embryonic stages of lower animals. c. pass through stages unique to only their phylum. d. none of the above. 2. Diploblastic animals lack a. true mesoderm b. true endoderm c. true ectoderm d. germinal epithelium 3. Crossing over occurs during which stage of meiosis a. prophase I. b. prophase II. c. anaphase I. d. none of the above 4. You discover a Drosophila embryo with no apparent head, but with tails at both ends. A plausible explanation is a mutation that inactivated the gene. a. nanos b. bicoid c. Pax6 d. distal-less 5. Cell-cell adhesion is often mediated by a. carbohydrates b. cadherins c. catenins d. all of the above 6. RNA interference pathways probably evolved in response to a. hybridization. b. cross fertilization. c. double stranded RNA viruses. d. double stranded DNA viruses. 7. Morpholino-antisense oligomers differ from normal antisense RNA in that they a. degrade quickly, so that transient effects can be studied. b. do not degrade quickly, so that long-term effects can be studied. c. can be visualized using fluorescent microscopy. d. are unable to enter the nucleus. 1
8. If a set of tissues is transplanted to an area of unlike fate, but retains its original fate, the original tissue was considered a. specified and determined b. specified but not determined c. determined but not specified d. determined but not committed 9. A characteristic of stem cells is that they each a. make multiple types of differentiated cells. b. make all types of differentiated cells. c. regenerate copies of themselves. d. die after undergoing mitosis. 10. 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. d. all of the above. 11. 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. 12. 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. 13. 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 14. TFIID, TFIIB, and TFIIA a. bind to the core promoter. b. form a portion of the transcription initiation complex. c. bind RNA polymerase II. d. all of the above. 15. In an example of stepwise induction, development of the frog lens requires a. the universal competence factor, Pax6. b. contact with the hindbrain and forebrain regions. c. induction by pharyngeal endoderm and mesoderm, then anterior neural plate. d. induction by neural retina and optic nerve. 2
16. 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. 17. 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. 18. 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. 19. 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. 20. 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 True / False (one point each) 21. Few tissues require multiple inductions. True / False 22. Apoptosis is always initiated by paracrine signals. True / False 23. Adding a methyl group to histones generally increases gene activity. True / False 24. In Drosophila the syncytial blastoderm stage is followed by the cellular blastoderm stage.true / False 25. The light bands seen in polytene chromosomes are heterochromatin. True / False 26. In deuterostomes the mouth originates from the blastopore. True / False 27. Nuclear hormone receptors are a sub-family of transcription factors. True / False 28. Long non-coding RNAs operate exclusively in cis to interfere with RNA transcription. True / False 3
29. Both long- and short-non-coding RNAs regulate Hox gene activity during development. True / False 30. Cytosine methylation inhibits DNA transcriptional activity in the roundworm C. elegans. True / False Fill in. (one point per answer) Use the terms from the Term Bank to make the most accurate sentence. Term Bank antibiotic resistance argonaut autocrine blasts committed stem cells delta dermal dimers fate germ histone acetyltransferase histone deacetylase hnrna juxtacrine methylase morphogen mosaic notch phosphodiesterase pluripotent stem cells protein-protein interaction domain RISC RNA sirna syncytium TAF TATA box TFIID transposable elements transfection 31. RNAi techniques make use of the cellular enzyme argonaut, which is part of the RISC complex. 32. Committed stem cells can produce committed stem cells but not pluripotent stem cells. 33. Dicer-deficient mice do not survive development, indicating the importance of sirna. 34. TAF proteins stimulate transcription by binding TDIID and acting as a histone acetyltransferase. 35. Notch signaling involves proteolytic cleavage after binding the _delta ligand in a _juxtacrine manner. 4
Define. Write a brief definition of any five of the following terms or phrases (2 points each): 36. Syncytium Nuclear division without cell division. 37. Multipotent stem cells Cells that produce several different types of committed progenitor cells, as well as copies of themselves. 38. Signal transduction The process of transmitting a signal from the outside of a cell, through the membrane, into the cytoplasm, and often into the nucleus, where it is translated into changes in gene expression. 39. Genetic specificity of induction The limitation on the ability of an inducing tissue (often mesenchyme) to change the fate of a responding tissue (often epithelia), that is determined by the genetic makeup of the responding tissue. 40. Reciprocal induction A common phenomenon in which a tissue induces a second tissue towards a new fate, which then acts as to induce the original tissue towards a new fate. 41. Trans-acting transcriptional regulator Any gene regulatory mechanism that involves entities (e.g. proteins or RNA) that are not a part of the proximate DNA strand. 42. Lyon hypothesis In female mammals both X chromosomes are initially active, but one, chosen randomly, is inactivated early in development, and it remains inactive in all of the cell s progeny. 43. Chimera An organism that developed from inner cell mass cells (embryonic stem cells) originating from two different sources. 5
Short Answer. Answer any six questions. Be certain to address all parts of the questions. (5 points each) 44. The presence of imprinted genes is one factor that prevents parthenogenesis in mammals. Explain this effect. Imprinting (methylation) silences genes; therefore, chromosomes with imprinted genes will lack the ability to produce transcripts at those loci. Since male and female genomes are differentially imprinted, a combination of the two sets will complement each other, filling in active alleles for the imprinted alleles contained in the other set. Parthenogenic organisms are produced without the contribution of the male genome, and could provide a complete genome if all of the female genes are active. However, in mammals some of the genes imprinted in females are necessary for early development, so parthenogenic embryos do not survive. 45. Your experiment to produce transgenic mice resulted in 25% that showed no trace of the transgene trait, 50% that showed partial expression of the trait, and 25% that died before birth. What conclusions can you draw from this data? Since the offspring showed the effects of the transgene, it must have been incorporated into the primordial germ cells (gamete precursor cells). However, the transgene was lethal in the homozygous condition. Your results show a Punnett square distribution with 25% wild type (no effect), 50% heterozygotes (partial effects), and 25% homozygous for the transgene (lethal) 46. Arrange the following gene features in their proper order: exons and introns, leader sequence, polya addition site, promoter region, TATA box, transcription initiation site, transcription termination site, translation initiation site, translation termination site, upstream promoter region upstream promoter region, promoter region, TATA box, transcription initiation site, leader sequence, translation initiation site, exons and introns, translation termination site, polya addition site, transcription termination site 47. Explain the significance of the partial success of experiments using serial transplantation of blastomeres to support amphibian cloning. Nuclei from older embryos supported short-term, but not long-term development in somatic nuclear transplantation (cloning) experiments. However, if nuclei from the surviving early stages were re-transplanted, survival times increased. These results indicated that differentiated somatic nuclei could de-differentiate and regain at least partial potency. 6
48. Although Dictyostelium is a very simple organism, its developmental life cycle has parallels to systems in more complex animals. Describe how one phase or behavior shown during the Dictyostelium life cycle is similar to a behavior found in the development of a higher organism. 1) aggregation, pseudoplasmodium formation, migration intracellular signaling, directed cell movement similar to that seen during gastrulation 2) specification of stalk or spore similar to specification throughout development 3) stalk and spore formation differentiation, morphogenesis, organ formation 4) chemotaxis similar to paracrine signaling in metazoans 5) spore formation - gametogenesis 49. Describe four mechanisms that differentiated cells might use signal transduction pathways or control of gene transcription to maintain their differentiated state. 1) A signal initiates the production of a transcription factor which stimulates the transcription of its own gene. 2) A signal stimulates the production of a protein that permanently opens the chromatin keep a promoter accessible. 3) A signal stimulates an autocrine loop within a cell, in which the cell manufactures the ligands for its own receptors. 4) A signal initiates a paracrine loop between two cells; the first produces a ligand for the second, which reciprocates by producing the ligand for the first. 50. 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. - The promoter sequence might not bind general transcription factors or RNA polymerase II with high affinity. If the preinitiation complex does not stay together, transcription will not progress. - The preinitiation complex may not bind accessory proteins (e.g. TAFs) that serve to stabilize the transcription factors and open up the chromatin. - The promoter may not be associated with enhancer elements, which accelerate transcription. 51. Describe the technique used to create reporter genes, and explain how they are used. The structural (coding) portion of a gene of interest is replaced with a gene whose product can be detected. Such products include luciferase, which can produce a light signal, β-galactosidase, which will turn certain substrates blue, and green fluorescent protein. When gene activity is stimulated via the intact regulatory region(s), the signal can be detected. Thus, normal gene activation can be traced via the reporter signal 52. Describe the molecular structure of chromatin. Chromatin consists of long chains of nucleosomes, which are DNA strands tightly associated with several types of histone proteins. Histone octomers, consisting of 4 homodimers of histone H2A, H2B, H3, and H4, form bead-like structures, around which 140 bp-long DNA strands are wrapped and electrostatically bound. Histone H1 monomers associate with the DNA strand outside the octomers. A 60 bp stretch of linker DNA connects each nucleosome. The nucleosome chains are coiled multiple times, eventually forming the highly compact chromatin structure 7
Short Essay. Answer 53 and one other question (10 points each). Be certain to address all parts of the questions and provide complete answers. 53. You are studying the effects of chemical X on Dictyostelium. You suspect that chemical X prevents Dictyostelium myxamoebae from specifying as spore cells if used during the migrating pseudoplasmodium stage, but that it doesn t have any effect once the culmination stage begins. Please design an experiment to test this hypothesis. You can assume that everything you need is available; mature Dictyostelium cultures, plates with E. coli lawns, microscopes, etc. are all provided. In addition, you have a solution of chemical X in water. Address the following points in your experimental design: A) State a hypothesis for your experiment. B) Describe briefly the experimental technique you would use to test the hypothesis. C) Describe the necessary control experiments that you would conduct. D) Briefly describe the expected outcome, and explain their relevance (i.e. explain what a successful experiment would prove) 8
54. Draw the receptor tyrosine kinase signal transduction pathway. A) 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. A) 1. ligand binding 2. receptor dimerizes 3. receptor autophosphorylation 4. adaptor protein activation 5. GNRP activation 6. RAS activation (GDP to GTP) 6a. GAP recycles RAS-GDP 7. RAF activation 8. MEK activation 9. ERK activation 10. ERK activates transcription factor B) Proto-oncogenes are genes that, if inappropriately activated, can trigger cancers. Ras, Raf, Mek, and Erk are considered proto-oncogenes. C) e.g. - ligand-receptor binding low concentration of ligand or weak binding - adaptor protein and other pathway intermediates low concentration; weak binding - Ras low concentration of GDP, low concentration or weak activity of GAP protein - transcription factors low concentrations - gene methylation or other factors producing tight association with nucleosomes 9
55. 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. Morphogens are diffusible molecules that stimulate cells towards certain fates. If a morphogen is produced in a certain tissue or site (a source), it will diffuse to areas of lower concentration (sinks), thus forming a concentration gradient. According to the morphogen gradient model of regeneration, cells will be specified according to their position within the gradient; i.e. different fates will be specified depending on the concentration of the morphogen. Regenerating a complex organ or structure requires multiple morphogen gradients. According to the polar coordinate model each cell has an identity that is defined by its position within the organism. Thus, each cell may have multiple coordinates that establish its position (e.g. longitudinal, latitudinal, or proximodistal). A newly regenerating cell acquires its positional identity and specification by sensing its relationship with its surrounding cells and tissues. Gaps within tissues are filled through intercalation. 10