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Biochemistry chp.21 RNA T/P
Review of chapter 21 (Transcription and RNA Processing)
17
Chemistry
Undergraduate 3
12/04/2008

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Term
Transcription:
Definition
- The sequence of DNA bases is recorded as a sequence of complimentary bases in a single stranded mRNA molecule.
 
  • DNA-dependent RNA synthesis
    • requires a DNA template.
Term
RNA Polymerase Overall Reaction:
Definition
[image]
Term
RNAP Holoenzyme:
Definition
  • Five core subunits:
    • [image] α
    • β
    • β' (active site)
    • ω
    • σ
  • No proofreading 3'-5' exonuclease
    • Error rate of RNA synthesis: 1 error per 104 to 105 bases polymerized
  • Synthesizes all three classes of RNA in E. coli.
Term
Template/Primer Requirements:
Definition
  • No primer required to initiate RNA synthesis.
  • DNA template required to determine identity of new nucleotides by Watson-Crick base pairing.
Term
RNA Synthesis:
Definition
  • Initiation of RNA synthesis occurs at specific DNA sequences in the genome called promoters.
  • Nt numbering: +1 is the first base pair to be copied into RNA.
Term
Promoter binding specificity (σ subunit):
Definition
  • σ subunit determines sequenc-specificity of DNA binding.
  • Several σ isoforms with differing sequence specificities and molecular weights.
  • σ disociates from the core RNAP during elongation.
Term
Promoter Functions:
Definition
  • Determination of the +1 base
  • Choice of template strand and overall direction of transcription.
  • Control of frequency of transcription initiation: strong versus weak promoters.
Term
Stages in transcription:
Definition
  • Initiation
    • Promoter binding by RNA polymerase (RNAP) to form closed complex.
    • Open complex formation (local melting of dsDNA at the+1 position.)
    • Initial RNA synthesis
  • Elongation
  • Termination
Term
E. coli transcription termination:
Definition
  • ρ-dependent termination:
    • The ρ RNA:DNA helicase disrupts the transcription bubble.
  • ρ-independent termination:
    • Structure of the RNA:DNA heteroduplex is less stable at certain sequences, which predisposes the transcription bubble to disassemble
    • Self-complementary sequence in the transcript followed by a run of A/U base pairs, just prior to the 3' end of the transcript.
Term
DNA-dependent RNAP in Eukaryotes:
Definition
  • RNAP I: pre-rRNAs
  • RNAP II: mRNAs (primarily)
    • Bind and transcribe from a variety of promoter sequences, which show a great range of promoter strength.
  • RNAP III: tRNAs, 5S rRNA
    • Certain portios of the promoter sequence are located within the coding sequence.
Term
Regulation of E. coli RNAP binding to promoters:
Definition
  • Activator proteins:
    • Facilitate RNAP binding to a specific promoter - increases the frequency of transcription initiation.
    • e.g. cAMP-receptor protein (CRP)
  • Repressor proteins:
    • Block RNAP synthesis from specific promoters - reduce the frequency of transcription initiation.
    • e.g. Lac repressor
Term
mRNA processing in eukaryotes:
Definition
  • Synthesis of primary transcript in the nucleus.
  • Synthesis of a "cap" at the 5' terminus
  • Cleavage and poladenylation of 3' terminus
  • Removal of introns by splicing
  • Transport of processed (mature) mRNA to cytosol for translation into protein
    • These events are catalyzed by large protein and protein/RNA complexes
  • Eventual degradation.
Term
RNA splicing:
Definition
  • Introns
    • Internal sequences removed from the primary RNA transcript.
  • Exons
    • Sequences that are present in the primary RNA and in mature RNA
Term
Self-splicing RNAs (two groups):
Definition
  • Gropu I:
    • Mitochondrial, chloroplast and some nuclear rRNAs, tRNAs and some mRNAs
    • Cofactor: Guanine nucleoside or nucleotide
  • Group II:
    • Mitochondrial and chloroplast mRNAs
    • Cofactor: an adenylate residue within the intron sequence.
Term
Viral-encoded reverse transcriptase:
Definition
  • Three enzymatic activities:
    • Copies the viral RNA into an RNA:DNA heteroduplex (RNA-dependent DNA polymerase).
    • Degrades the RNA half of the RNA:DNA duplex.
    • Copies the DNA copy of the genome to make a dsDNA version of the viral genome (DNA-dependent DNA polymerase).
Term
Retroviral Protease:
Definition
  • Cleaves polyproteins to generate the mature active proteins required for viral particle assembly andreplication
  • The "protease inhibitors" used to treat HIV infections inhibit this enzyme and thus interrupt the viral replication cycle.
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