Chapter 13 Genetic code and transcription

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  1. Genetic code is
    • written in linear form
    • uses ribonucleotide bases that compose mRNA molecules as letters
  2. Triplet codons
    • in mRNA it specifies one amino acid
    • codon contains "start" and "stop" signals, certain codons (nonsense codons) that are necessary to initiate and to terminate translation
    • provides 64 codons to specify the 20 amino acids
  3. Main characteristics of genetic code is
    • unambiguous
    • degenerate
    • commaless
    • nonoverlapping
    • nearly universal
  4. What serves as an intermediate in transferring genetic information from DNA to proteins?
  5. frameshift mutations
    revealed triplet nature of the code
  6. Nonoverlapping and commaless
    genetic code reads three nucleotides at a time in a continous, linear manner
  7. Degenerate genetic code
    • some amino acids are specified by more than one codon
    • only tryptophan and methionine are encoded by a single codon
  8. Nonsense codons
    do not specify an amino acid
  9. Polynucleotide phosphorylase
    an in vitro protein synthesizing system along with the ability to produce synthetic mRNAS along with polynucleotide phosphorylase provided means for deciphering the genetic code
  10. RNA homopolymers
    RNA nucleotides with only one type of ribonucleotide
  11. Nirenberg and Matthaei
    added RNA homopolymers to the in vitro translation system to decipher which amino acids were encoded by the first few codons based on which amino acids were incorporated into the polypeptide
  12. RNA heterpolymers
    two or more different ribonucleosides were used to decipher more codons employing the same method
  13. Triplet binding Assay
    • developed by Nirenberg and Leder
    • determined other specific codon assignments
    • in this technique, ribosomes bind to the single codon of 3 nucleotides and the complementary amino acid charged tRNA will be able to bind
  14. Wobble hypothesis
    • predicts that the initial two ribonucleotides of triplet codes are often more critical than the third
    • thrid position of the codon-anticodon interaction would be less spatially constrained and need not adhere as strictly to the established base-pairing rules at the third position of the codon
  15. N-formylmethionine (fmet)
    formylated methionine that is found in prokaryotes
  16. Termination codons
    • UAG, UAA, and UGA
    • don't have an associated amino acid
  17. MS2
    • bacteriophage with only three genes on a 3500 base RNA genome
    • specify a coat protein, an RNA-directed replicase, and a maturation protein
    • sequencing of the gene products confirmed the genetic code
  18. What type of DNA revealed some exceptions to the universal genetic code?
    mitochondrial DNA
  19. Open reading frame (ORF)
    overlapping genes in some viruses have been identified in which initiation at different AUG positions out of frame with one another leads to distinct polypeptides
  20. RNA polymerase
    • directs synthesis of RNA using a DNA template
    • no primer required for initiation
    • enzyme uses ribonucleotides instead of deoxyribonucleotides
  21. E. coli RNA polymerase contains what subunits
    alpha, beta, beta prime, omega, sigma
  22. Promoter
    site at which transcription begins with the template binding by RNA polymerase
  23. Omega subunit
    responsible for promoter recognition (initiation of transcription)
  24. Transcription start site
    start site where the DNA double helix is unwound to make the template strand accessible to the action of RNA polymerase
  25. Consensus sequences
    • TTGACA and TATAAT (the two E. coli promoters)
    • positioned at -35 and -10 with respect to the transcription initiation site
  26. Mutations in any region do what?
    diminish transcription, often severely
  27. Chromatin remodeling
    eukaryotic transcription requires chromatin to become uncoiled, making the DNA accessible to RNA polymerase and other regulatory proteins
  28. Transcription factors
    eukaryotic RNA polymerases rely on TFs to scan and bind to DNA
  29. In addition to promoters, what else control transcription regulation?
    enhancers and silencers
  30. What 3 steps are required to produce mature mRNAs
    addition of a 5' cap, addition of a 3' tail, and excision of introns
  31. RNA polymerase II
    • repsonsible for a wide range of genes in eukaryotes
    • have a core promoter element and promoter that determines where RNP II binds to the DNA and where it begins copying the DNA into RNA
  32. What factors influence the efficiency or rate of transcription initiation?
    three regulatory DNA sequences, proximal-promoter elements, enhancers and silencers
  33. TATA box
    core promoter element  that binds to the TATA-binding protein (TBP) of transcription factor TFIID and determines the start site of transcription
  34. Enhancers and silencers
    • can be upstream,within, or downstream of the gene
    • can modulate transcription from a distance
    • act to increase or decrease transcription in response to cell's requirement for a gene product or at a particular time during development or place within an organism
  35. General transcription factors
    absolutely required for all RNP II-mediated transcription
  36. Transcription activators and repressors
    influence the efficiency or the rate of RNP II transcription initiation
  37. Two broad categories of transcription factors that facilitate RNP II binding and initiation of transcription
    General transcription factors and transcription activators and repressors
  38. Heterogeneous nuclear RNA (hnRNA)
    • posttranscriptionally processed before it can leave the nucleus
    • addition of 5' cap that protects from nuclease attack and may be invovled in the transport of the transcript across the nucleus
    • poly-A tail added to aid transport to cytoplasm
    • Introns are removed by splicing
  39. Introns
    • intervening sequences
    • regions of the initial RNA transcript that are not expressed in the amino acid sequence of the protein
    • removed by splicing and exons are joined later together in the mature mRNA
  40. Is mature mRNA or initial RNA smaller
    mature mRNA
  41. Spliceosome
    • splices out pre-mRNA intron
    • reaction involving the formation of a lariat structure
  42. Two main types of RNA editing prior to translation:
    substitution editing and insertion/deletion editing
  43. Substitution ending
    the identities of individuals nucleotides bases are altered; prevalent in mitochondria and chloroplast RNA derived in plants
  44. Insertion/deletion editing
    nucleotides added/deleted from the total number of bases
  45. Polyribosomes have been observed in
    both prokaryotes and eukaryotes
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Chapter 13 Genetic code and transcription
2013-10-28 22:44:21

Ch 13 genetic code
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