BIOL360 Eukaryotic Gene Regulation

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BIOL360 Eukaryotic Gene Regulation
2011-08-21 15:51:16
Eukaryotic Gene Regulation

BIOL360 Eukaryotic Gene Regulation
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  1. True or False. All the cells in your body have the same genes.
  2. What is considered the most important level of regulation?
    Initiation of Transcription
  3. Regulation of Transcription Initiation is divided into what two levels?
    • Basal Level Transcription
    • Regulated Expression
  4. What is Basal Level Transcription?
    • It is driven by the interaction of:
    • Core Promoter Elements
    • General Transcription Factors
    • RNA Polymerase II
  5. What is Regulated Expression?
    • It is driven by the interaction of:
    • Promoter Proximal Elements
    • Enhancers
    • Activators & Repressors
    • (Things that modify Basal Level)
  6. In tightly packaged chromatin, the basal level of transcription is what?
  7. Eukaryotes have how many RNA Polymerases?
  8. What does Polymerase I transcribe?
    5.8S, 18S, and 28S rRNA genes
  9. What does Polymerase III transcribe?
    • 5S rRNA
    • tRNA
    • several other small genes
  10. What does Polymerase II transcribe?
    Protein Coding Genes
  11. Eukaryotic mRNAs encode how many polypeptide each?
    One polypeptide
  12. Eukaryotic mRNAs are generally LESS or MORE stable than Prokaryotic mRNAs?
    MORE stable.
  13. The default state for most Prokaryotic genes is what?
  14. The default state for most Eukaryotic genes is what?
  15. What is the major form of gene regulation?
    Transcription Initiation
  16. Name three Eukaryotic cis-elements.
    • Enhancers
    • Promoter Proximal Elements
    • Core Promoter
  17. Where are Enhancers often located?
    Thousands of BPs upstream or downstream of a gene, even within the transcription unit it regulates.
  18. What type structure do Transcription Regulatory Proteins of Eukaryotes have?
    Modular Structure
  19. Regulatory Transcription Factors have some combination of what kinds of Functional Domains?
    • DNA Binding Domain
    • Domain that interacts Basal Level
    • Domain that binds with other Specific Transcription Regulatory Proteins
    • Domain that alters Chromatin condensation
    • Domain that senses a physiological state
  20. Coregulators do what?
    Help alter Chromatin condensation
  21. Coregulators are recruited by what?
    Transcription Factors
  22. What is a Transcription Factor?
    A sequence of specific DNA binding protein that somehow alters the rate of transcription at a gene.
  23. What are Coregulators?
    They are recruited to genes by Transcription Factors but do not bind directly to DNA. They indirectly regulate the rate of transcription.
  24. What bind to Promotor Proximal Elements and Enhancers and change the rate of Transcription?
    Activators & Repressors
  25. Specific Transcription Factors act in what ways?
    • They can bind & help recruit GTFs or the Polymerase to the Promoter.
    • They can bind & help recruit Chromatin Remodeling Complexes to the region.
    • They can bind & help recruit Histone Modifying Enzymes to the region.
    • They can bind to other TFs & alter their activities.
  26. What is a model of Eukaryotic gene regulation?
    GAL system in Budding Yeast
  27. What genes are used by Saccharomyces cerevisiae to enconde enzymes to convert galactose to glucose?
    • GAL1
    • GAL2
    • GAL7
    • GAL10
  28. In S. cerevisiae, each of these are controlled by a SINGLE or SEPARATE regulatory sequences?
  29. Does S. cerevisiae have Operons?
  30. What are the Regulatory Proteins for the expression of the GAL1, GAL2, GAL7, and GAL10 genes?
    • GAL3
    • GAL4
    • GAL80
  31. What is the equivalent of enhancers in yeast?
    Upstream Activator Sequence (UAS)
  32. What binds to UAS elements associated with GAL genes?
    GAL4 Transcriptional Activator Protein
  33. GAL4 transcription activator protein has what kind of structure?
  34. GAL4 Protein contains what?
    Structurally and functionally separable DNA binding and transcription activation domains
  35. What happens in S. cerevisiae in the absence of glucose?
    Gal80 protein binds and blocks the function of the Gal4 activation domain
  36. What happens in S. cerevisiae in the presence of glucose?
    Gal3 protein facilitates the release of Gal80, exposing the Gal4 activation domain.
  37. What does the Gal4 activation domain do?
    Recruits RNA pol II
  38. How does Gal4 activation domain recruit RNA pol II?
    By binding to TFIID & Mediator
  39. What is a Mediator?
    A coactivator complex
  40. In Eukaryotic chromosomal DNA, what can inhibit transcription initiaton?
    Nucleosomes in Chromatin
  41. What is required for Transcriptin Eukaryotes regarding Chromatin?
    • Chromatin Remodeling
    • Histone Modification
  42. Each nucleosome contains two copies of the core histones. What are the core histones?
    • H2A
    • H2B
    • H3
    • H4
  43. Are Core Histones Highly Basic, Neutral, or Highly Acidic?
    Highly Basic (+)
  44. Histone H1 does what?
    Binds to the Linker DNA between Histones
  45. Chromatin Remodeling requires what kind of energy source?
  46. Chromatin Remodeling does what?
    • Repositions nucleosomes or
    • Alters the interaction of histones and DNA within a nucleosome
  47. What is an example of a Histone Remodeling Complex?
  48. SWI/SNF can be recruited to specific sites by what?
    • Transcription Factors or
    • Acetylated Histones
  49. What is an example of a TF that recruits SWI/SNF?
  50. What is the best studied form of Histone Modification?
    Acetylation of Histone Tails by Histone Acetyltransferase (HAT)
  51. What does Acelyation of Lysine Residues do within the histone tails?
    It lessens the attraction between histones and DNA and provides binding sites for several proteins involved in transcription.
  52. What can Histone Acetylation be reversed by?
    Histone Deactylases (HDACs)
  53. How does the presence of Glucose repress expression of the GAL genes?
    Mig1 protein binds a DNA sequence found between the UAS and the GAL1 promoter. Mig1 then recruits the HDAC containg corepressor complex Tup1 to the gen, resulting in a more condensed chromatin structure.
  54. Enhancers contain what?
    Binding sites for multiple specific transcription factors.
  55. What is an Enhanceosome?
    A large complex created by TFs bind to the Enhancer
  56. Enhanceosomes help recruit Transcriptional Machinery by bind what?
    Coactivator Complexes
  57. How can Enhancers act at a distance from the promoter?
    They can loop out the intervening DNA and interact with proteins in the promoter region.
  58. What prevents Enhancer Activation?
    Enhancer-Blocking Insulators
  59. How do Enhancer-Blocking Insulators work?
    Insulators segregates regulatory sequences into separate loops of chromatin preventing them from interactin with each other.
  60. In maternal impriting, the copy of the gene inherited from WHICH parent is inactive?
    the Mother
  61. In paternal impriting, the copy of the gene inherited from WHICH parent is inactive?
    the Father
  62. An imprinted gene will be expressed as if there were how many copies present in the genome?
  63. What is the most common DNA modification in higher eukaryotes?
    The modification of cytosine to form 5-methylcytosine
  64. About how many of the C's are methylated?
  65. The methyl group on the methylated C does not alter base pairing, but it can alter the ability of a DNA binding protein to recognize a sequence HOW?
    Because it protrudes into the Major Groove
  66. What kind of relationship (proportional or inverse) exists between the degree of Methylation an the degree of Gene Expression?
  67. Genomic imprinting was discovered how?
    Because of the unusual inheritance of imprinted genes.
  68. What are two examples Epigenetic Information?
    • DNA Methylation
    • Covalent Modification of Histones
  69. How can epigenetic information be inherited?
    Through Mitosis or from Parent to Offspring
  70. For Epigenetic Information to be Inherited, where must the information be preserved?
    In the daughter molecules each time DNA replication occurs.