Bio 400 final

  1. Does RNA need a primer for transcription?
  2. What are the three phases of the RNA transcription?
    Initiation, elongation and termination.
  3. When looking at the DNA strand there are -34 or +34 for example (number doesn?t matter) what do they represent?
    (-) How many bases behind transcription and (+) how many bases after transcription.
  4. What is it that binds to the promoter sequence for Polymerases?
    Holoenzyme plus some promoter recognition sites
  5. This is the ore enzyme complex, plus a sigma factor that binds to promoter sequences.
  6. What is another name for sigma factor? And what is the most common in E. coli?
    S factor ad s70
  7. This is an extra sequence to help promote RNA pol recruitment; binds to flexible CTD of alpha subunit of core enzyme.
    Upstream promoter element (UP)
  8. Describe the initiation stage of RNA pol?
    RNA pol recruited to promoter, RNA binds to promoter while duplex remains closed. DNA duplex opens up (melts). Then nucleotides brought to active site so transcription can begin.
  9. Melting of the DNA duplex in the promoter is mediated by?
    Interaction with s factor
  10. Where does the melting happen?
    Just upstream of the first copied DNA base, inside the -10 motif.
  11. This promoter element can promote or discourage RNA pol binding via s factor, making promoters stronger or weaker?
  12. The -10 motif where DNA melts is rich with what and why?
    Thymine and adenine. Easier to bend and open up TATAA box
  13. Fist steps of elongation: this domain is displaced by DNA duplex. Slightly negative like the DNA backbone and will only open when the charged active site arrives.
    Sigma 1.1 then the dna is melted
  14. Initial to elongation: RNA strands up to 10bp are easy to make longer are harder. This blocks the RNA chair until it reaches 10bp. Must be displaced to make way for a longer RNA chain to proceed through the exit.
    Sigma ?
  15. What are the ways to terminate transcription?
    Rho-independent (intrinsic) and Rho-dependent
  16. This method of termination involves making a stem and loop in the RAN transcript. Structure disrupts elongation by RNA pol, triggering release
  17. RNA transcript has sequence (poorly defined) that recruits Rho ATPase (another hexamer). Rho uses energy from the ATP hydrolysis to disassemble RNA pol elongation complex.
    Rho-dependent (Rho climbs up the RNA to RNA poly and pulls the RNA out.
  18. What are some regulatory proteins?
    Activators and repressors
  19. Changes in protein conformation in response to binding another molecule.
  20. DNA binding proteins that promote/repress RNA pol actively; these must identify and bind specific sequences, so transcription factors commonly bindin the major groove of DNA.
    Transcription factors (TFs)
  21. Region of DNA that directs RNA polymerase activity toward downstream coding sequences to be transcribed.
  22. Region immediately upstream of coding sequence that most directly regulates RNA pol activity, mostly by physically positioning RNA pol.
    Core promoter.
  23. DNA region that binds repressor proteins to inhibit transcription
  24. Region of DNA downstream of coding sequence that directs RNA polymerase to stop transcription and release.
  25. Multiple discrete protein coding sequences under control of a common promoter.
    Polycistronic operon.
  26. Eukaryotes transcription: What are the similarities to prokaryotes?
    Initiation, elongation, and termination. Bulk of regulation is at initiation.
  27. Eukaryotes transcription: What is different from prokaryotes?
    Three different RNA pol. Multiiple general transcription factors (GTF) required not one. Chromatin structure influences DNA accessibility and splicing.
  28. What are some characteristics to the GTF?
    Regulatory elements can be far away, Huge mediator complex
  29. Main focus on RNA transcription in Eukaryotes is on?
    RNA pol II
  30. Eukaryotes transcription: describe the RNA pol II promoter site.
    Multiple sites for the components of the GTF complex. Initiation complex begins at TATA box
  31. Eukaryotes transcription: what are all the components for the promoter site?
    Inr, BRE, TATA, TBP, DCE, and DPE
  32. What is the Inr?
    Initiator element
  33. What is the BRE?
    TFIIB binding element
  34. What is the TATA?
    TATA box where DNA unwinds
  35. What is the TBP?
    TATA box binding protein. Sub unit of TFIID
  36. What is the DCE?
    Downstream core element
  37. What is the DPE?
    Downstream promoter element
  38. Eukaryotes transcription: transciption factor that contains TBP as subunit. Other subunits are TAFs. Is the first to bind ; provides a platform to recruit.
  39. Eukaryotes transcription: Transcription factor that makes contacts with both TBP and DNA. Also contracts pol II. Bridge from TBP to pol II.
  40. Eukaryotes transcription: transcription factor that enters the complex at the same time as pol II. Required before TFIIR and TFIIH can join.
  41. Eukaryotes transcription: transcription factor that binds next and recruits TFIIH
  42. Eukaryotes transcription: transcription factor that is helicase to unwind the DNA and has kinase to phosphorilare CTD of the pol II.
  43. These are critical triggers for the initiation of transcription in eukaryotes.
    Helicase and kinase
  44. Eukaryotes transcription: this helps position RNA pol II, integrates signals from many possible activators/repressors, etc.
  45. Phosphorylation of the RNA pol II tail CTD controls many steps like?
    As a scaffold to recruit enzymes for each stage of TXN. Capping enzymes, components of splicing machinery, and polyadenylation and cleavage factors.
  46. What are the three steps of capping?
    Remove 5? game phosphate of RNA. 2 attach guanine to 5? end of RNA. (5?-5?) 3 modify guanine with methyl group.
  47. Eukaryotes transcription: what are the models of termination?
    Torpedo and allosteric
  48. Eukaryotes transcription: mode of termination 5? to3? RNase enzyme attacks remain in transcript after cleavage. RNase enzyme ?bumps? RNA pol II and forces dissociation.
  49. Eukaryotes transcription: mode of termination inherent dissociation when RNA transcription is shortened, conformational change in RNA pol.
  50. Eukaryotes transcription: transcription activators almost always have at least 2 functional domains.
    DNA binding domain (DBD) and activation domain (AD).
  51. Eukaryotes transcription: promoters commonly have redundancies for?
    Activator binding sites
  52. Eukaryotes transcription: DNA binding domain example 1. Dimer of two long helices; look like pinchers. Hydrophobic side chains pack between the two helices at the dimer inaction interface. Both helices extend and occupy the major grooves on either side.
    Leucine zipper.
  53. Eukaryotes transcription: DNA binding domain example 2. Another dimer. One helix stabilizes dimer interface. One helix fits into major groove, side chains identify specific DNA sequence.
  54. Eukaryotes transcription: making gene sequences permanently inaccessible to transcription factors. Methylated cytosine in a promoter region.
    Gene silencing
  55. Eukaryotes transcription: Methylated signals are often maintained as cells replicate. Freshly synthesized daughter strands would not be methylated, so duple is hemimethylated.
    Silenced genes inheritance
  56. Eukaryotes transcription: enzymes probe for hemimethylated sites, add more methyl groups to local cytosines.
    Maintenance of methylase
  57. Eukaryotes transcription: basic mechanism of removing exons and introns. Splicing machinery.
  58. Eukaryotes transcription: these are what code for proteins.
  59. How are exons ad introns marked to guide splicing?
    SR proteins and hnRNP.
  60. These proteins mark exons (short stretches)
    Serine-arginine proteins SR proteins
  61. The proteins tend to mark introns (long stretches)
    Heterogenous nuclear ribonucleoproteins hnRNP
  62. What is the inventory of Mature RNA?
    5? cap, poly A tail, splicing done, Exons present( SR complexes Exon junction complexes), and introns absent ( few hnRNOs attached.
  63. What is the difference between Prok and Ek mRNA?
    Prok have RBS and EUK have 5?cap and pol A tail.
  64. Big cytotoxic ribonucleoprotein complexes that execute translation
  65. What are the parts of the ribosome?
    2 subunits 50s and 30s or p and 60s and 40s E. 3 tRNA binding pockets. EPA
  66. How fast is transcription?
    60NT per s
  67. How fast is translation?
    20 AAs per sec
  68. Adaptor molecules to connect specific codons to specific amino acids.
    Transfer RNA
  69. This is in prokaryotes that is immediately upstream of start codon AUG
    RBS ribosome binding site
  70. Pairing of 16s rRNA to RBS sequence positions the ribosome P-site?
    Directly on top of the start codon
  71. Initiator tRNA (tRNAi). This has just one codon.
    UAC (AUG)
  72. Determine the reading from of a coding sequence
    Start codons AUG
  73. Initiator amino acids: Prokaryote and eukaryote
    EUK: methionine and PUK; N-formal methionine (fMet)
  74. These help prep he small subunit in Prok. Ribosomes to initiate translation.
    Initiation factors aka IF
  75. How my different Ifs are there?
    IF3, IF1, IF2
  76. This IF blocks the big subunit assembly
  77. This IF blocks A-site
  78. This IF helps recruit initiator tRNA; blocks non-initiator tRNAs ? Gtpase
  79. Prok: Phase of translation 30s initiation complex. Small subunit, mRNA, fMet-tRNAi, IF1-3
    Phase 1
  80. Prok: phase of translation. 30s initiation complex shed IF3. Big sub unit assembles. Assembly triggers GTP hydrolysis by IF2. IF1 and 2 exit. A-site ready
    Phase 2
  81. Initiation in EUK: two sets of eIFs doing two jobs?
    Prep small ribosome subunit to encounter mRNA and prep mRNA for recognition and translation
  82. There are many components for the prep of initiation in EUK they have some jobs what is it?
    Block association with big subunit, block A site, recruit charged initiator tRNA and GTPase Smith present to trigger disassembly later.
  83. EUK: mRNA preparations. Tell meeessss?
    Identify the 5? cap, helicase activity (smooth out and unwind) and provide binding sites for the small subunit.
  84. EUK: elongation. These proofread the codon-anticodon pairing
  85. EUK: elongation. These power translocation
  86. EUK: this resets the ribsomal complex after a peptidyletransferase reaction
  87. Often calla a robot witch RNA molecule whose #D folding creates a binding pocket for a specific ligand; naturally occurring riboswitches frequently bind to a molecule related to function of the protein encoded by the mRNA
  88. An apt amber (RNAmolecule)that posses catalytic activity, so it can covert substrate into product.
  89. Bacterial/prokaryotic, short RNA that binds to protein ormRNA to regulate function. Typically 80 to 110 bases of non-coding sequences.
  90. Eukaryotic, process whereby double-stranded RNA sufficient length is targeted for destruction (by Dicer), the resulting cleavage products are used to probe and destroy more mRNA of compatible sequence by 9RISC complex)
  91. Eukaryotic, endogenously produced (chromomally encoded) short RNA molecule that can base pair with mRNA for post-transcriptional regulation of gene expression.
  92. Same as miRNA, but exogenously produced and delivered to cells/organism, typically with the purpose of triggering RNAi for a selected gene/mRNA
  93. Bind a lot of common metabolites. MRNA sequence makes predictable 3D structure based on intramolecular base pairing. Ligand is often a substrate or product of the enzyme encoded by the mRNA. Translation can be inhibited or activated.
  94. What happens when a riboswitch binds its ligand molecule?
    Shape change. Base-pairing shuffle or rearrange. RBS will be hidden or revield.
  95. Thought to have evolved as a defense mechanism vs retroviruses, many of which dsRNA genomes.
    • DsRNA is chopped up by a dicer into small chunks.
    • RNA interference (RNAi)
  96. This loads siRNA from dicer cleavage, surveys cytoskeleton fro complimentary RNA molecules to destroy.
  97. In many EUK this extends the siRNA using the complimentary, longer RNA as a template, making a longer dsRNA
    RdRp (RNA-dependent RNA polymerase)
  98. Where do miRNA come from?
    Commonly processed from longer RNA molecules, pre-miRNA, RNA introns, RNA exons, UTRs, and non-coding RNAs.
  99. Encodes a protein that, if over-produced, promotes cancer
    Oncogenes mRNA
  100. MicroRNA reduces abundance or translation of onogenic mRNA
    Tumor suppressor miRNA
Card Set
Bio 400 final
bio 400 final