Genetics Chapter 13

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Genetics Chapter 13
2012-07-29 13:12:23
Genetics Chapter 13 Dr Troy Bray

Genetics Chapter 13 Dr. Troy Bray
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  1. Who was the first to suggest a relationship between genes and the production of proteins (enzymes)?
    Archibald Garrod
  2. Garrod studied patients with what disease?
  3. What is the one gene-one enzyme theory?
    a single gene controlled the synthesis of a single enzyme
  4. Who proposed the one gene-one enzyme theory? What organism did they work with?
    • George Beadle and Edward Tatum 
    • mutated fungi
  5. How did following researchers modify the one gene-one enzyme theory?
    • enzymes are only one category of cellular proteins encoded by a gene
    • some proteins are composed of two or more polypeptides
  6. Why is it more accurate to say that a structural gene encodes a polypeptide not necessarily a protein?
    polypeptide denotes structure and protein denotes function
  7. What is a codon?
    groups of three nucleotides on mRNA that codes (mostly) for a particular amino acid 
  8. What is an anticodon?
    found on tRNA and recognizes/corresponds to codons on mRNA
  9. What is the start codon and what does it code for?
    • AUG 
    • methionine 
  10. What are the stop codons?
    • UAA
    • UAG
    • UGA 
    • *do not code for an amino acid 
  11. Why three nucleotides per codon? Why not two?
    if it only coded for 2, it could only code for 16 amino acids and there are 20. having 3 gives you multiple ways to code for an amino acid 
  12. How is the genetic code degenerate?
    because the number of possible codon combinations (64) exceeds the number of possible amino acids (20)
  13. What is a synonymous codon?
    two codons that specifiy for the same amino acid
  14. What are codon families comprised of?
    synonymous codons
  15. What position base is the wobble codon?
  16. Researchers have found the genetic code to be almost universal. What type of DNA is slightly different?
    mtDNA in mammals
  17. What is the reading frame?
    • the start codon (AUG) defines the reading frame of any mRNA
    • indels shift the reading frame and it alters the amino acids creating a different polypeptide 
  18. What is the N-terminus and the C-terminus?
    • amino terminus end
    • carboxyl terminus end
  19. What is the primary protein structure
    the sequence of a chain of amino acids
  20. What is the secondary protein structure?
    • occurs when a sequence of amino acids are linked by hydrogen bonds
    • alpha helix and beta pleated sheets
  21. What is the tertiary protein structure?
    occurs when certian attractions are present between alpha helices and pleated sheets
  22. What is the quartinary protein structure?
    a protein consisting of more than one amino acid chain
  23. How are tRNA molecules named?
    • according to the amino acid they carry
    • i.e. tRNAphe
  24. What are some common features of tRNA?
    • 3 stem loop structure
    • a few vairiable sites
    • acceptor stem with 3' single stranded region CCA sequence
    • anticodon in 2nd stem loop
    • ~75 nucleotides long
  25. If the anticodon in the tRNA is 5'-CGG-3', what would the complementary codon be?
  26. What is a charging tRNA?
    • amino acid and ATP bound to enzyme; AMP binds to amino acid and pyrophosphate (PPi) is relseased
    • activated aminio acid is attachd to the 3' end of tRNA at acceptor stem and AMP is released from enzyme
  27. What is the error frequency of a charging tRNA?
    1 in100,000
  28. What is the wobble hypothesis?
    • first 2 positions of codon adhere strictly to the AT/CG rule
    • 3rd position can tolerate certain mismatches
    • 1st position of the anticodon can move slightly so that hydrogen bonding can occur between mismatched codon and andticodon
  29. What are isoacceptors?
    • two or more tRNAs that are able to recognize the same codon
    • i.e. anticodon (CCA or CCG) both recognizes single codon GGU
  30. What gives additional flexibily to the tRNA molecule?
    • the structure of bases in tRNAs (especially wobble position) can be modifed into less common nucleosides
    • wobble interactions between anitocodon and codons
    • G pairs with C or U
    • C pairs with G
    • A pairs with A or G
    • U pairs with A or G
    • I (inosine) pairs with A, U, or C
  31. Describe bacterial ribosome.
    • sinlge type 
    • found in cytoplasm
    • 1/3 cell mass
  32. Describe eukaryotic robosomes.
    • biochemically distinct ribosomes
    • most abundant type functions in the cytosol
    • unique, smaller ribosomes are found in teh mitochondria and chloroplasts
  33. What is the structure of rRNA?
    • composed of a large and small subunit
    • overall shape result of rRNA since it constitutes most of the mass
  34. What is the interface between the small and large subunits primarily composed of?
  35. What clusters on the outer suface of the ribosome and on the periphery of the interface?
  36. Bacterial ribosome= ___S
    Small subunit= __S with ___ different proteins and ___S rRNA 
    Large subunit= ___S with ___ different proteins and two rRNa (___S + ___S)
    • 70S
    • 30S, 21, 16S
    • 50S, 34, 23S, 5S
  37. Eukaryotic ribosome= ___S
    Small subunit= ___S with ___ differnt proteins and __S rRNA
    Large subunit= ___S with ____ different proteins and ___S + ___S rRNA
    • 80S
    • 40S, 33, 18S
    • 60S, 49, 5S and 5.8S
  38. What are the tRNA binding sites?
    • peptide site (P site)
    • aminoacyl site (A site)
    • exit site (E site)
  39. Overview of initiation.
    mRNA, initiator tRNA (bound to start codon), and ribosomal subunits assemble
  40. Overview of elongation.
    ribosome slides along mRNA in 5' to 3' direction moving over the codons sequentially linking amino acids brought in by tRNA
  41. Overview of terminaion.
    stop codon signals the termination of translation at which time the polypeptide is released and ribosomal complex disassembles
  42. Describe the initiation stage in bacteria.
    • the initiator tRNA is designated tRNAfmet because the methioinine has been modified
    • a formyl group (__CHO) is attached to the nitrogen atom in methionine after it has been attached to the tRNA
    • Shine-Dalgarno sequence promotes hyrdogen bonding of mRNA to the 30S subunit
  43. What is the Shine-Delgarno sequence?
    a sequence that is complementary to a short sequence withing the 16S rRNA
  44. What three factors are required for mRNA, tRNAfmet, and ribosomal subunits to associate into initiation?
    • IF1 (initiation factor)
    • IF2
    • IF3
  45. What does IF1, IF2, and IF3 do?
    • IF1- separates and prevens premature binding of 30S and 50S subunits
    • IF2- binds fmet-tRNA to 30S and binds to GTP
    • IF3- binds 30S to mRNA
  46. Describe initiation in eukaryotes.
    • additional intitation factors are required
    • eIF designation for eukaryotes
    • initiator tRNA carries methionine instead of formylmethionine
    • eIF binds directly to tRNAmet prior to recruitment of 40S subunit
  47. How are eukaryotic mRNAs recognized by the ribosome since there is no Shine-Delgarno sequence?
    • Cap-Binding protein I (CBPI) binds to 7-methylgranosine cap on mRNA and recruits other initiation factors
    • these initation factors unwind any secondary structures in mRNA and promote binding to ribosome
  48. Where to start translation?
    • after binding, ribosome slides along mRNA downstram of 5' cap searching for AUG codon
    • it will not always start at the first AUG codon, it depends what is around it
  49. What is Kozak's rule?
    • consensus sequence for optimal translation initiation
    • three places upstream tends to be a G and right next to the start codon is a g
  50. When does the elongation process begin?
    when the start codon is identified and the 60S subunit assembles with the aid of eIF5 
  51. Describe the elongation process.
    • amino acid added one at a time to the growing polypeptide chain
    • 15-18 amino acids per second in prokaryotes
    • 6 amino acids per second in eukaryotes
    • GTP hydrolysis is required
    • 3 elongation factors involved
  52. When does termination occur?
    when stop codon (nonsense codon) is reached in mRNA
  53. What is the stop codon recognized by?
    proteins known as release factors which mimic the structure of tRNA
  54. How many release factors are needed to recognize the three stop codons in bacteria? In eukaryotes?
    • multiple RF
    • a single release factor (eRF)
  55. Describe the final step in termination.
    • disassembly if mRNA, ribosomal subunits, and the release factor
    • RF binds to site A
    • bond between polypeptide and tRNA is hyrodylzed releasing it from the ribosome
  56. What are polyribosomes?
    • mRNA transcript tht has many bound ribosomes in the act of translation 
    • in bacteria, translation can occur before transcription is finsihed
  57. Kanamycin
    • interferes with correct wobble base pairing
    • prevent correct pairing of codon and anticodon
    • prevent aminoacyl-tRNA binding at A site
    • prevents EF-Tu disassociation from ribosome and process stalls in initiation phase 
    • premature chain termination
    • blocks E-site
  58. What are sorting signals?
    signals that direct amino acids into correct location 
  59. Why is the process more complex in eukaryotes?
    because of the compartmentalization
  60. What is cotranslational sorting? posttranslational sorting?
    • sorting that can occur during tranlation
    • sorting that can occur after translation is complete