Biolchem 415: Lec. 34

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Biolchem 415: Lec. 34
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2015-04-28 21:48:22
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University of Michigan Biolchem 415: Lecture 34 Flashcards
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  1. What is the flow of genetic information from DNA to protein?
    • DNA --transcription->RNA--translation->protein
    • DNA--replication->DNA
  2. What is a gene?
    A region of DNA transcribed to produce a functional RNA molecule
  3. What is gene expression in eukaryotes characterized by?
    • 1. complex transcription regulation
    • 2. rna processing (especially rna precursors)
    • 3. nuclear membrane
  4. What does the nuclear membrane in eukaryotes do?
    Separates site of RNA synthesis from protein synthesis
  5. Describe RNA/protein synthesis in prokaryotes.
    mRNA is translated while it is being transcribed
  6. Describe RNA/protein synthesis in eukaryotes.
    • Transcription and most RNA processing in the nucleus. 
    • mRNAs are exported to the cytoplasm where translation into protein occurs
  7. How many RNA polymerases do eukaryotes have?
    3
  8. What is α-Amanitin?
    RNA polymerase poison produced by mushrooms
  9. How does α-Amanitin destroy RNA polymerase?
    Binds near the active site of RNA pol and prevents translocation along DNA
  10. What is the effect of α-Amanitin on (eukaryotic) RNA pol I, II, and III; the cellular transcripts; and locations?
    • I: insensitive; 18S, 5.8S, and 28S rRNA, nucleolus
    • II: strongly inhibited; mRNA precursors and snRNA; nucleoplasm
    • III: inhibited by high concentrations; tRNA and 5S rRNA; nucleoplasm
  11. Why are eukaryotic and prokaryotic RNA polymerases similar?
    Use an identical catalytic mechanism with Mg2+
  12. What is snRNA, what is its size and function?
    Small nuclear RNA, has less than 300 nucleotides, and is a component of RNA splicing machienery
  13. What is snoRNA, what is its size and function?
    Small nucleolar RNA, less than 300 nucleotides, and rRNA biogenesis and modification
  14. What is miRNA, what is its size and function?
    MicroRNA, 20-25 nucleotides, regulates use of mRNA
  15. What is siRNA, what is its size and function?
    Small interfering RNA, 20-25 nucleotides, antiviral defense against mRNA degredation
  16. What is piRNA, what is its size and function?
    Piwi-interacting RNA, 29-30 nucleotides, gene regulation
  17. What is lncRNA, what is its size and function?
    Long noncoding RNA, greater than 200 nucleotides, gene regulation
  18. What do ribosomal and transfer RNA (rRNA/tRNA) function for?
    Protein synthesis.
  19. How are eukaryotic promoters more complicated than bacterial promoters?
    Each RNA pol has distinct promoters

    Each euk. RNA pol has to find specific promoter in billions of DNA nucleotides

    Transcription regulated to produce right amount of RNA at right time and place
  20. How is transcription in eukaryotic RNA polymerase regulated?
    Cis acting elements (ex: promoters/enhancers): DNA sequences that control transcription of a gene are are located on the same molecule of DNA

    Transcription factors: proteins that regulate gene expression
  21. What types of RNA pol II promoters are there?
    TATA containing and TATA-less promoters.
  22. Describe a TATA-less promoter.
    Found in RNA pol II, has enhancer upstream, an initiator element (Inr), and either a TATA box or a downstream promoter element (DPE) downstream
  23. What do enhancers do? In what RNA polymerases are they commonly found?
    Bind transcription factors to regulate gene expression, separate from promoter regions in RNA polymerase II.
  24. Where is RNA polymerase I found and what does it do?
    Located in nucleolus and transcribes genes for rRNA.
  25. What is a key feature about RNA polymerase I?
    Large, coordinated quantities of rRNA needed to generate ribosomes
  26. How many arrays do humans have of RNA pol I?
    5 arrays of 300-400 rRNA genes
  27. What is the setup of the RNA pol I promoter?
    Promoter= UPE + rInr

    • UPE: upstream promoter element (~150 bp upstream)
    • rInr: ribosomal initiator element: lies just upstream of initiation site
  28. What is the setup of RNA pol I?
    28S-----UPE---rInr-----18S---5.8S--28S
  29. What is the nucleolus?
    Ribosome producing factory within the nucleus?
  30. What does RNA pol III do?
    Synthesizes RNA and 5S ribosomal RNA
  31. Where are promoters in RNA pol III?
    Promoters within the transcribed sequence, downstream of start site
  32. Large quantities of ________ must be produced by eukaryotic cells to generate _________.
    5S rRNA, ribosomes
  33. How many tRNA genes do eukaryotes have?
    • Euk: hundreds of tRNA genes
    • ~500 in humans
  34. Describe the type I RNA pol III promoter.
    A block and C block nearby leads to transcription
  35. Describe the type II tRNA RNA pol III promoter.
    A block and B block downstream leads to transcription
  36. What binds to promoters to regulate gene expression?
    Transcription factors
  37. What is TFII? What are their individual names?
    Set of transcription factors for RNA pol II; TFIIA, TFIIB, etc.
  38. What must genes have for there to be transcription factors that bind to the TATA box?
    TATA box, TATA box-binding protein (TBP), a component of TFIID
  39. What is the order in which TFII binds to the promoter (TATA box)?
    1. TFIID, 2. TFIIA, 3. TFIIB, 4. TFIIF, 5. RNA pol II, 6. TFIIE, 7. TFIIH

    DABFpolEH--What does the Canadian bear say to the hiker when he is stuck in the honey pot?

    Do A Bear a Favor and Pull, EH?
  40. What does TFIIH do?
    Opens DNA double helix in eukaryotes
  41. What does TFIIH do?
    Phosphorylates the carboxyl-terminal domain (CTD) of RNA pol II. Allows polymerase to leave the promoter and begin transcription
  42. Why is TFIIH important?
    Facilitates the transition from initiation to elongation phase
  43. Where do transcription factors bind?
    Enhancers and promoter regions
  44. What do promoter regions often contain?
    Transcription factor binding sites
  45. Why do enhancers contain multiple binding sites for transcription factors?
    Different transcription factors recognize different sequences
  46. T/F: Specific transcription factors regulate only one target gene.
    False. may regulate hundreds of different target genes
  47. What are enhancers?
    Cis-acting elements that have no promoter activity, but can stimulate transcription from promoters
  48. Where are enhancers located?
    Close or far. Can be thousands of nucleotides from the start site.
  49. Give an example of enhancer regulation.
    Hemoglobin regulation--tissue specific expression of 5 beta hemoglobins. Transcription controlled by enhancers in the Locus Control Region (LCR) and promoters
  50. What are transcription factors?
    Bind to specific DNA sequences to regulate gene expression
  51. What are coactivators?
    Bind to transcription factors to facilitate transcription by RNA polymerase II.
  52. What are mediators?
    Large complex of proteins that act as a bridge between enhancer-bound activators and proteins, including polymerase, at the promoter
  53. What are other proteins that play a role in transcription regulation?
    • 1. DNA binding regulatory proteins (activators/repressors)
    • 2. DNA looping
    • 3. Combinatorial control
  54. Describe the DNA binding regulatory proteins: activators and repressors.
    Activators: bind enhancers, stimulate transcription of a gene.

    Repressors: reduce or prevent transcription of a gene
  55. How does DNA looping regulate transcription?
    Allows enhancers to come into contact with promoters
  56. Describe combinatorial control.
    Multiple regulators working together. Different effects on transcription depending on components already bound to enhancer and promoter
  57. How can transcription factors control cell identity?
    Pluripotent stem cels can differentiate after stimulation
  58. How are induced pluripotent stem cells (iPS) generated from cells?
    Insertion of genes for only 4 specific transcription factors--Sox2, Oct4, cMyc, and Klf4
  59. What are other ways gene expression can be regulated?
    Steroid hormones
  60. What does estradiol do?
    Controls the genes in the development of female secondary sex characteristics and reproductive cycle
  61. How does estradiol exert its effects?
    Forms a complex with a specific receptor protein called estrogen receptor
  62. What is the estrogen receptor part of?
    Regulatory protein: nuclear hormone receptor, which are activated by binding of small molecules or ligands
  63. What are DNA binding domains?
    Zn-finger domains that confer specific DNA binding.
  64. What do nuclear hormone receptors bind to?
    Specific regions of DNA called response elements
  65. What does the estrogen receptor bind to?
    Estradiol response element (ERE)
  66. What does a ligand binding domain cause?
    Structural change that enables the receptor to recruit other proteins to regulate transcription
  67. What does the nuclear hormone receptor act as?
    Hormone-responsive transcriptional switch
  68. How do nuclear hormone receptors control transcription?
    Recruit corepressors or coactivators
  69. Y/N: Does ligand binding alter the ability of the nuclear hormone receptors to bind DNA?
    No
  70. In the unbound form, some receptors bind to corepressors and inhibit transcription--what happens upon hormone ligand binding?
    Repression stops and transcription starts. Ligand-bound form of the receptor may recruit a coactivator that stimulates transcription
  71. What are agonists?
    Ligands that activate nuclear hormone receptors
  72. What are antagonists?
    Ligands that inhibit a nuclear hormone receptor
  73. What are some forms of breast cancer dependent on?
    The estradiol-receptor complex
  74. What antagonists can breast cancer? What is the group called?
    Antagonists to the estrogen receptor: tamoxifen and raloxifene. Selective estrogen receptors modulators (SERMS)
  75. How does histone modification remodel chromatin?
    DNA is packaged by chromatin, which can impede transcription
  76. What can coactivators do to histone modified chromatin?
    Stimulate transcription by loosening interactions between histones and DNA. Makes the DNA more accessible to transcriptional machinery
  77. How can histones be modified?
    Methylation, phosphorylation, etc.
  78. What do Histone AcetylTransferase enzymes (HATS) do?
    Modify histones. Components of coactivators or are recruited by coactivators.
  79. What does acetylation do?
    • Reduces the affinity of histones for DNA. Generates docking site for proteins with bromodomains.
    • Recruitment of additional components of transcriptional machinery
    • Recruitment of chromatin-remodeling machines, ATP powered complexes that make DNA in chromatin more accessible
  80. In what steps does chromatin remodeling facilitate transcription
    • 1. Recruitment
    • 2. Acetylation of histone tails
    • 3. Recruitment
    • 4. Remodeling of chromatin structure
    • 5. Recruitment
  81. How can histone tails be modified?
    Acetylation, methylation, phosphorylation, ubiquitination
  82. What do histone deacetylases contribute to?
    Transcriptional repression and compaction of chromatin
  83. T/F: Only some covalent modifications of histones are reversible
    F: all covalent modifications are reversible
  84. What do HDACs do?
    Histone deacetylase enzymes catalyze the removal of acetyl groups from histones to inhibit transcription
  85. What does dark-stained heterochromatin indicate?
    Deacetylated histones that are densely packed. Inactive or repressed genes
  86. What does light-stained euchromatin indicate?
    Actively transcribed genes

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