transcripFINAL.txt

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cooxcooxbananas
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179375
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transcripFINAL.txt
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2012-10-23 16:35:50
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transc
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  1. A gene is defined as...
    a segment of DNA that is used to make a functional product, either an RNA molecule or a polypeptide.
  2. Transcription is the act of...
    "making a copy"
  3. In Transcription, you synthesize ____ from ____.
    RNA from DNA
  4. Transcription adds nucleotides to...
    the growing 3' end of an RNA chain
  5. In DNA, a promoter is...
    The site for RNA polymerase binding.
  6. What signals the begining of transcription?
    Promoter
  7. What signals the end of transcription?
    Terminator
  8. What is the three steps in the "central dogma" of genetics?
    • 1) DNA Replication
    • 2) Transcription
    • 3) Translation
  9. DNA replication produces..
    Chromosomal DNA
  10. Chromosomal DNA stores....
    information in units called genes
  11. Trancsription produces..
    Messenger RNA
  12. Messenger RNA is a...
    temporary copy of a gene that contains information to make a polypeptide
  13. Translation produces..
    A polypeptide
  14. Polypeptides become a part of...
    functional protein that contributes to an organism's trait
  15. List the flow os genetic infromation in the central dogma of genetics from start to finish.
    • 1) DNA Replication
    • 2) Chromosomal DNA
    • 3) Transcription
    • 4) Messenger RNA
    • 5) Translation
    • 6) Polypeptide
  16. What is gene expression at the molecular level?
    The overall process by which the information within a gene is used to produce a functional product.
  17. What causes RNA synthesis to occur within a defined location?
    The promoter and terminator sites
  18. What are the regulatory sequences of DNA?
    sites for binding of regulatory proteins.
  19. What is the role of regulatory proteins?
    to influence the rate of transcription.
  20. The DNA strand that is copied is termed the...
    Template Strand (non coding)
  21. The opposite DNA strand is called the...
    Coding strand (sense strand)
  22. The base sequecne of the coding strand is _________ the RNA transcript
    identical to
  23. RNA Polymerase is..
    The enzyme that catalyzes the synthesis of RNA
  24. in a transcription bubble there is about ____ bp of DNA/RNA hybrid.
    8
  25. In a transcription bubble there is about ____ bp of unpaired DNA.
    17
  26. What is a core enzyme?
    a RNA Polymerase without the sigma factor
  27. What are the four subunits of the core enzyme?
    two alphas, A beta and a beta prime (a2bb')
  28. In addition to the four subunits, what are the two other subunits that the core enzyme may include?
    δ and ω (delta and omega)
  29. What is capable of transcribing DNA into RNA randomly?
    Core enyzme
  30. The core enzyme is capable of transcribing DNA into RNA......
    randomly
  31. What is a holoenzyme?
    A holoenzyme is a core enzyme with an added sigma factor
  32. What is specificity?
    When the subunit allows RNA polymerase to recognize promoters
  33. Core enzyme does not recognize...
    promoters
  34. What are the three stages of transcription?
    • Initiation
    • Elongation
    • Termination
  35. What happens in Intiation?
    The promoter functions as a recognition site for initiation
  36. What happens in Elongation?
    RNA polymerase slides along the DNA in an open complex to synthesize the RNA transcript in the 5’ to 3’ direction
  37. What happens in termination?
    A termination signal is reached that causes RNA polymerase to dissociated from the DNA.
  38. In intiation, Following the binding of RNA polymerase to the promoter, the DNA is..
    denatured into a bubble known as the open complex.
  39. Promoters are DNA sequences that __________ gene expression.
    "promote"
  40. Promoters direct the exact location for the initiation of transcription by....
    telling RNA polymerase where to bind on the DNA
  41. _________ direct the exact location for the initiation of transcription by telling RNA polymerase where to bind on the DNA
    promoters
  42. The position in DNA where the RNA chain starts is called...
    +1
  43. DNA 5' to the start site is called..
    Upstream
  44. DNA 5' to the ________ is called Upstream.
    start site
  45. ______ to the start site is called upstream.
    DNA 5'
  46. Upstream is given ______ values.
    Negative
  47. Downstream is given _____ values
    Positive
  48. DNA to the 3' side is called ....
    downstream
  49. DNA to the ____ side is called downstream.
    3'
  50. The sigma subunit recognizes the ____ and the ___ regions of a promotoer on both DNA strands.
    -10 and -35
  51. The sigma subunit recognizes the -10 and -35 regions of a promoter on....
    Both DNA strands
  52. what is the promoter region consists of from left to right?
    -35 sequence, 16-18bp, -10 sequence
  53. what is to the right of the promoter?
    Transcriptional start site
  54. The first nucleotide that acts as a template for transcription is located at the...
    transcriptional start site
  55. The first nucleotide that acts as a template for transcription is called...
    +1.
  56. The nucleotide that is immediately to the left of the +1 nucleotide is numbered..
    –1
  57. the nucleotide that is immediately to the right of the +1 nucleotide is numbered..
    +2
  58. There is no ____ nucleotide in the promoter numbering system.
    zero "0"
  59. The binding of the RNA polymerase to the promoter forms...
    the closed complex
  60. the open complex is formed when...
    ~17 bp of DNA in the vicinity of the TATAAT box is unwound
  61. What is abortive initiation?
    When Many short RNAs (2-10 nucleotides) are made within the open complex without any movement of RNA polymerase.
  62. What is promoter clearance?
    When RNA polymerase eventually moves away from the promoter 5’ to 3’
  63. When is the sigma factor released?
    when promoter clearance takes places
  64. What marks the end of initiation?
    When the sigma factor is released
  65. What are the 4 steps of transcription initiation?
    • 1) Binding of RNA polymerase holoenzyme to form a closed complex
    • 2) Formation of an open complex
    • 3) Release of sigma factor
    • 4) Promoter clearance
  66. RNA is snythesized in a 5' to 3' direction using _______ as a precursor
    ribonucloside triphosphates
  67. When RNA is snythesized, ______ is released.
    pyrophosphate
  68. why is pyrophosphate released when RNA is snythesized?
    because ribonuceloside triphophates are used as a precursor
  69. In the synthesis of the RNA transcript, The RNA polymerase slides along the DNA creating an ________ as it moves.
    open complex
  70. In the synthesis of the RNA transcript, The __________ slides along the ______ creating an open complex as it moves.
    • RNA polymerase
    • DNA
  71. In the synthesis of the RNA transcript, The DNA strand known as the template strand is used to make....
    a complementary copy of RNA as an RNA-DNA hybrid.
  72. In the synthesis of the RNA transcript, The DNA strand known as the ___________ is used to make a complementary copy of RNA as an RNA-DNA hybrid.
    template strand
  73. In the synthesis of a RNA transcript, RNA polymerase moves along the template strand in a ________ direction.
    3′ to 5′
  74. What are the two different mechanisms for transcription termination?
    Intrinsic termination and rho-dependent
  75. Which transcription termination only requires sequences in the DNA -> RNA?
    Intrinsic termination
  76. Which transcription termination is factor independent?
    Intrinsic termination
  77. Which transcription termination is rho independent?
    Intrinsic termination
  78. Which transcription termination is rho dependent?
    pho-dependent termination
  79. Intrinsic termination depends on....
    two sequences in the RNA
  80. What are the two sequences in RNA that intirnsic termination depends on?
    • 1) A uracil rich sequence located at the 3' end of the RNA
    • 2) A stem-loop structure upstream of the Us
  81. What acts as the recognition site for the binding of the rho protein?
    a sequence upstream from the terminator, called the rut site.
  82. What are the three steps in rho-dependent termination
    • 1) rho-protein binds to the rut site in RNA and moves toward the 3' end.
    • 2) RNA polymerase reaches the terminator and a stem-loop causes RNA polymerase to pause
    • 3) RNA polymerase pauses due to its interaction with the stem-loop structure and the rho protein catches up to the open complex and separates the RNA-DNA hybrid
  83. What happens in intrinsic termination?
    The stem-loop causes RNA polymerase to pause and the U-rich sequence is not able to hold the RNA-DNA hybrid together. (termination occurs)
  84. In intrinsic transcription termination, The DNA template strand goes through ________ to make RNA transcript.
    Transcription
  85. In intrinsic transcription termination, The DNA template strand goes through transcription to make .....
    RNA transcript
  86. In intrinsic transcription termination, the RNA transcript goes through _________ to make folded RNA.
    Rapid RNA Folding
  87. In intrinsic transcription termination, the RNA transcript goes through Rapid RNA folding to make...
    Folding RNA
  88. In intrinsic transcription termination, _______ helps cause chain termination
    Folded RNA
  89. In intrinsic transcription termination, Folded RNA helps cause....
    chain termination
  90. In bacteria, what event marks the end of the initiation stage of transcription?
    The release of the sigma factor
  91. A consensus sequence is...
    is the calculated order of most frequent residues in nucleotides
  92. An Up-promoter mutation is..
    Any mutation allowing a mutated nucleotide in the core promoter sequence to look more like the consensus sequence
  93. A down-promoter mutation is..
    Any mutation allowing a mutated nucleotide in the core promoter sequence to look less like the consensus sequence
  94. A mutation within a gene sequence changes the start codon to a stop codon. How will this mutation affect the transcription of this gene?
    It won't
  95. A mutation within a gene sequence changes the start codon to a stop codon. How will this mutation affect the translation? of this gene?
    It will prevent the synthesis polypeptide synthesis
  96. Sigma factor can slide along the _______ groove of the DNA.
    major
  97. How is the sigma factor able to recognize base sequences that are exposed in the major groove of the DNA?
    Sliding along the najor groove
  98. What happens when a sigma factor encounters a promoter sequence?
    hydrogen bonding between the bases and the sigma factor protein can promote a tight and specific interaction
  99. hydrogen bonding between the ____ and the sigma factor protein can promote a tight and specific interaction.
    Bases
  100. hydrogen bonding between the bases and the _________ protein can promote a tight and specific interaction.
    Sigma factor
  101. ___________ between the bases and the sigma factor protein can promote a tight and specific interaction.
    Hydrogen bonding
  102. What is the sequence in Pribnow's box?
    at the –10 region is 5ʹ–TATAAT–3ʹ

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