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Abigail Leslie Biochemistry Undergraduate English 92 cards

Cards in this deck (92)

  1. 1Upstream (negative numbers)Nomenclature, DNA on the template/nontemplate strand that is before the initiation point of transcription
  2. 2Downstream (positive numbers)Nomenclature, DNA on the template/nontemplate strand that is before the initiation point of transcription
  3. 3Template StrandThe DNA strand that is being used to synthesis mRNA
  4. 4Nontemplate StrandThe DNA strand that is not being used to synthesize RNA, and is attached to the Template strand
  5. 5PromoterSite of transcription initiation
  6. 6EnhancerEukaryotes - site on DNA where transcription factors bind. More distant than in bacteria
  7. 7OperatorBacteria - Site where transcription factors bind. Closer than in Eukaryotes
  8. 8TerminatorSite of transcription termination
  9. 9Steps of Initiation1. Start: RNA polymerase binds promoter
    2. RNA pol separates DNA strands - txn bubble
    3. First few NTPs (rNTPs) added
    4. RNA pol moves past the promoter and changes conformation to be more stably associated with the DNA
  10. 101. Start: RNA polymerase binds promoter 2. RNA pol separates DNA strands - txn bubble 3. First few NTPs (rNTPs) added 4. RNA pol moves past the promoter and changes conformation to be more stably associated with the DNAList the steps of Initiation
  11. 11ElongationRNA pol moves along the DNA and adds
    ribonucleotides
    • Unwinds DNA ahead of it, and DNA repairs
    • Short region of transcript is paired with DNA; the rest of the RNA is extruded from the polymerase
  12. 12Termination• RNA pol meets terminator sequence
    • Dissociates from the DNA
  13. 13RNA Pol IWhich RNA Pol is associated with ribosomal RNA (rRNA)?
  14. 14RNA Pol IIWhich RNA Pol is associated with mRNA?
  15. 15RNA Pol IIIWhich RNA Pol is associated with tRNA?
  16. 16Subunits assemble into a complex with jaw-like lobes, with the active site at the base of the cleftDescribe the structure of RNA pol
  17. 172 MG+s prepare the oncoming 3' OH by stabilizing O-, and stabilize the pyrophosphate intermediate.Describe how RNA pol catalyzes nucleotide addition. How is this similar to DNA Pol?
  18. 18TrueTrue/False: RNA pol II couples mRNA synthesis to mRNA processing?
  19. 19General Transcription FactorsRNA Pols need these extra proteins to target the core enzyme to promoter regions
  20. 20Pre-Initiation Complex (PIC)TFII Proteins assemble with RNA Pol II to form this
  21. 21TFIIThese transcription factors are associated with RNA Pol II
  22. 22TATA BoxA common Promoter motif for RNA Pol II
  23. 23TATA Binding Protein (TBP)Eukaryotic polymerases need this protein to initiate transcription. It is a part of TFIID
  24. 24TFIIDThe binding of this element to the TATA box is the first step in initiation.
  25. 25TBP-associated Factors (TAFs)These mediate the recognition of other promoter elements, like INR and DPE
  26. 26TFIIBThis element is recruited AFTER TFIID, and helps to determine the transcription direction
  27. 27TFIIABinds AFTER TFIID and TFIIB, this element binds and stabilizes TBP-DNA interactions
  28. 28TFIIE and TFIIHThese two elements bind last, after TFIIA, TFIIB, and TFIID
  29. 29TFIIHThis transcription factor binds last AND catalyzes the ATP powered unwinding of DNA
  30. 30Topoisomerase (TXN)This enzyme creates transient cuts in DNA in order to relieve torsional stress.
  31. 31Closed ComplexRNA pol (complex) + promoter (dsDNA)
  32. 32Open ComplexRNA pol + open DNA
  33. 33Abortive InitiationThis failure occurs frequently in transcription, due to the TFIIB loop being in the way
  34. 34Promoter ClearanceDisplacement of the TFIIB loop caused by phosphorylation of TFIIH
  35. 35TFIIH on SER5Kinase activity of this enzyme on this residue starts elongation and recruits capping enzyme
  36. 36P-TEFb on SER2Kinase activity of this enzyme on this residue resolves pausing after capping. (And is promoted by capping)
  37. 37Transcriptional PausingRNA polymerase stops during elongation due to a physical barrier. This is called:
  38. 38Transcriptional arrestWhen elongation has paused, and RNA synthesis cannot resume
  39. 39BacktrackingCan be caused by pausing
    -Most recent RNA protrudes from front of complex
    -the reverse polymerization reaction occurs (cleavage)
    This is thought to have a role in error correction
  40. 40FACT(Facilitates Chromatin Transcription)
  41. 411. Release transcript at proper intervals 2. Release the DNAWhat must RNA pol do at time of termination?
  42. 42Terminator SequencesIn DNA, these are the signal to cease transcription
  43. 43CPSFWhat cleaves the RNA after a terminator sequence?
  44. 44FalseTrue/False: After RNA is cleaved, RNA pol stops transcription
  45. 45Allosteric model of RNA pol termination-RNA processing proteins associate with the processing signals and the CTD
    -Cleavage or recognition of processing proteins
    -> conformational changes, Pol II dissociates from DNA
  46. 46Torpedo model of RNA pol terminationAfter cleavage, the RNA downstream of the poly(A) signal is digested by a 5′ to 3′ endonuclease (Rat1)
    • Rat1 degrades the nascent RNA until it runs into the RNA polymerase, disrupting polymerization and causing RNA pol to dissociate from the DNA
  47. 47Transcriptional RegulationWhat causes
    •Differentiation and development
    • Time
    • Cell type
    • Environmental changes
  48. 48RepressorRegulatory protein that decreases transcription
  49. 49ActivatorsRegulatory proteins that increase transcription
  50. 50Regulatory sequenceSpecific DNA in which regulatory proteins bind
  51. 51Operator sitesRegulatory sequences in bacteria are called
    ____ and are located close to the promoter
  52. 52EnhancersRegulatory sequences in Eukaryotes are called ____, are often more distal and can be located either upstream or downstream from the gene.
  53. 53Co-activator/Co-repressorCannot regulate/bind on their own, must be recruited by activators/repressors
  54. 54DNA binding domainDomain in activator/repressor that bind DNA.
  55. 55Allosteric binding Modification Abundance/LocalizationWhat can affect TFs
  56. 56Mediatior - Brings enhancer regions closer to the Initiation SiteWhat is 'required' for transcription?
    How does it work?
  57. 57Direct interaction, by preventing an activator from binding to an enhancer regionHow does direct interaction work for repression?
  58. 58Repressors can recruit other enzymes such as HDACs to prevent transcriptionHow does recruitment work for repression?
  59. 591. OCT4, 2. Sox2, 3. Klf4, 4, c-Myc Are four factors that are critical for cell differentiation.What are the OSKM factors?
    What do they do?
  60. 60They are often localized to tissues and low in abundanceWhat is true about the abundance of sequence specific TFs?
  61. 61An activating/repressing domain and a DNA-binding domainWhat domains does a specific sequence TF have?
  62. 62Interacts with major groove, First helix separated from recognition helix by short linker. An example is HomeodomainWhat is a helix-turn-helix DNA binding domain?
  63. 63An example of HTH DBD, a monomer. N-terminal interacts with major groove.What is Homeodomain?
  64. 64A DBD where an alpha helix and 2 beta sheets surround a central zinc atom. Most common, and many proteins have mutlipleWhat is a Zinc finger?
  65. 65Long alpha helices, dimers. 2 options, 1. coiled coils, and 2. splayed N-term helices that sit in the major groove.What is a (leucine) zipper?
  66. 66The basic region is disorderedWhat happens when a zipper isn't bound to DNA?
  67. 67A master TF controls cell identityWhat is a Master TF?
  68. 68A set of TFs that can form both Homo and Hetero dimers.What is Fos/Jun
  69. 69Fos/Jun heterodimer = AP1 • Proliferation (cell growth and division) • S phase genes have AP1 enhancersWhat is the Fos/Jun heterodimer used for>?
  70. 70Similar to bZIP • Dimerization often is a leucine zipper, always hydrophobicWhat is the difference in a helix-loop-helix DBD?
  71. 71open chromatinPoised promoter
  72. 72The Max/Myc heterodimer is the active transcription factor. To prevent transcription, Mad sequesters Max, making the dimer unable to form.How does the Mad/Max heterodimer work?
  73. 73[Trp] low = genes are transcribed • [Trp] high = Trp repressor binds to Trp operator and blocks RNA polymerase from binding • Dependent on high [Trp]What is the mechanism behind the Trp repressor?
  74. 74Elk-1 is an example of mediator recruitment in EukaryotesWhat is ELK-1 an example of?
  75. 75Mitogen absence: ELK1 binds to DNA and serum response factor (SRF), but doesn’t activate transcription Mitogen presence: Kinases phosphorylate ELK1, which then recruits MediatorHow does Elk-1 respond to Mitogen?
  76. 76Gal4 is an example of mediator recruitment in Eukaryotes, and coregulationWhat is Gal4 an example of?
  77. 77When Galactose levels are low, Gal80 bind to Gal4, causing Mediator to not be recruited, When Galactose levels are high, Gal3 sequesters Gal80, and Mediator is recruitedHow does Gal80 and Gal3 regulate Gal4?
  78. 78Gal4 was edited several times, and transcription was tested. When the DBD or activating regions were removed, no transcription occurred. When the activation region was removed, but a modified Gal80 with an activating region was added, transcription occurred.How was it proven that the DBD and activation site of Gal4 are independent?
  79. 79Common in activation domains, and are a large cluster of amino acids that are acidic and largely hydrophobicWhat is an acid blob?
  80. 80Production of HSP70. When transcription occurs, activation occurs normally but the regulation is at the transition to elongation, saving the cell both energy (not transcribing) and time (having parts in place)What is the Heat Shock response?
  81. 81It is the response of a gene to multiple transcription factors/regulatory subunits.What is combinatorial control?
  82. 82a and (a) (alpha) cells, and the a/(a) haploidWhat are the three types of yeast cells?
  83. 83a1, (a)1, (a)2, and MCM1What are the genes that control yeast cells?
  84. 84MCM1Which gene that controls yeast type is always present?
  85. 85MCM1, which controls the production of a genesWhat TFs are activated in an a type yeast cell
  86. 86(a)2 repressed a genes, (a)1 activates (a) genesWhat TFs are activated in an (a) type yeast cell, and what do they do?
  87. 87a1 and (a)2 genes form a heterodimer, and repressed haploid genes, including (a)1What TFs are activated in an a/(a) haploid?
  88. 88HMG proteins increase flexibility in DNA it is bound to.What do HMG proteins do?
  89. 89An activator that uses CCCTC binding factor, and regulates chromatin structure. CTCF is an insulatorWhat is CTCF?
  90. 90Cohesion is a protein ring that works with CTCF. DNA passes through this ring. This creates a chromatin loopWhat is cohesion? (the protein)
  91. 91A protein that binds to a ligand effector, and typically have a DBD and a ligand binding domain. Typically Homo or hetero dimers. Spacing determines specificityWhat is a nuclear hormone receptor?
  92. 921. Escape HSP90 and enter the nucleus or 2. Activate coregulatorsWhat are the two types/mechanisms of Nuclear Hormone Receptors

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An overview of Transcription and how it is regulated
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Abigail Leslie
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