MBS 6 Protein Synthesis

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MBS 6 Protein Synthesis
2016-08-28 17:29:36
MBS Biochemistry Exam 1
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  1. What subunits make up a eukaryotic ribosome?
    60S and 40S
  2. What is the sedimentation coefficient of eukaryotic ribosomes?
  3. The 60S ribosomal subunit contains which rRNAs?
    • 1) 28S
    • 2) 5.8S
    • 3) 5S
  4. The 40S ribosomal subunit contains what rRNA?
    1) 18S
  5. Why is the genetic code called degenerate?
    Because most of the 20 amino acids are coded for by more than one codon
  6. Where are ribosomes usually found in the cell?
    In the cytoplasm or attached to the endoplasmic reticulum
  7. What is the fate of proteins synthesized by ribosomes on the endoplasmic reticulum?
    They are either exported from the cell or become part of the cellular membrane
  8. tRNA factoids
    • •  each amino acid binds to one or several specific tRNA molecules
    • • all tRNAs contain approximately 80 nucleotides
    • • some residues base pair in any molecule resulting in a characteristic cloverleaf folding
  9. What is a codon?
    A trinucleotide sequence of mRNA that determines which amino acid is added to a nascent protein during translation
  10. What is the sequence of the start codon?
  11. The start codon codes for which amino acid?
  12. What are the sequences of the stop codons?
    UAA, UAG, and UGA
  13. What is the purpose of CCA on the tRNA?
    • • the final A (adenosine) is the site of attachment of the amino acid to the tRNA
    • • every tRNA has a CCA sequence at its 3' end
  14. What are the purposes of attaching an amino acid to the 3' of an appropriate tRNA molecule?
    • • formation of a peptide bond between the amino group of one amino acid and the carboxyl group of another is thermodynamically unfavorable
    • • energy barrier is overcome by activating amino acids by linking them to a hydroxyl group on a ribose unit at the 3' end of tRNA
  15. What are the purposes of attaching an amino acid to the 3' of an appropriate tRNA molecule?
    • -covalently links the amino acid to a tRNA containing the correct anticodon
    • -attachment activates the amino acid (generates a high energy linkage at its carboxyl end)
  16. Aminoacyl-tRNA synthetases
    class of enzymes that activate and attach amino acids to their respective tRNAs; they pair the correct amino acid with its corresponding tRNA; there's a different synthetase for every AA
  17. UTR
  18. What is the Wobble Hypothesis?
    There are fewer tRNAs than codons. It was proposed that the 3' end of the codon allows for a more relaxed bonding with the 5' base of the anticodon. The potential for non-Watson-Crick base pairing at this position allows a single tRNA to pair with several different codons.
  19. _________ _________ are the starting point for translation
    Ribosomal subunits, NOT ribosomes, are the starting point for translation
  20. Met-tRNA
    functions in the initiation process; unlike all other AA-tRNAs, it can bind to the small ribosomal subunit (40S) with the help of eIF-2, and the binding is NOT dependent on the presence of a codon for methionine
  21. In which direction does a ribosome read RNA?
    5' to 3' (the same direction as nucleic acid synthesis by DNA and RNA polymerases)
  22. eIF-2
    • binds to initiator Met-tRNA and GTP (eIF2-GTP-Met-tRNA) to bind to the small 40S ribosomal subunit and initiate translation
    • • once the anticodon of the initiator Met-tRNA and the AUG start codon match, the eIF-2 allows hydrolysis of GTP that enables the release of eIF-2 from the 40S subunit & allows the 60S subunit to join
  23. eIF4F
    recognizes + associates with the 5' m7G cap and positions the mRNA on the small 40S ribosomal subunit
  24. Which subunit first binds the the 5' end of a mRNA?
  25. How many tRNA binding sites are there on the ribosome?
    two: the P site contains tRNA attached to the GROWING poly-peptide chain, and the A site contains the INCOMING aminoacyl-tRNA
  26. What are the three sites that interact with tRNAs during elongation of a peptide?
    • A, P and E sites
    • • A site accommodates the incoming amino acyl-tRNA
    • • P site contains the peptidyl-tRNA complex (the tRNA still linked to all the amino acids added to the chain so far)
    • • E (exit) site is for empty tRNA that has been used
  27. What is a peptide bond?
    A covalent bond between an amino group of one molecule and the carboxyl group of another. Peptide bonds are formed between amino acids during protein synthesis.
  28. peptidyl transferase
    • • catalyzes the nucleophilic attack, by the amino group of the aminoacyl-tRNA in the A site, on the carbonyl of the activated ester linkage of the peptidyl-tRNA in the P site
    • • as a result, growing polypeptide chain is transferred to the tRNA in the A site
    • • a component of the 28S rRNA (a ribozyme)
  29. What is the purpose of elongation factors?
    Elongation factors (EF) position amino acyl-tRNAs on the ribosome and promote RNA translocation
  30. EF1
    • catalyzes the GTP-dependent binding of aminoacyl-tRNA to ribosomes, thereby regulating the fidelity and rate of polypeptide elongation during translation
    • • forms a ternary complex with the aminoacyl-tRNA and GTP that binds to the A site
    • • ("chaperones" this tRNA into the A site)
  31. EF2
    translocates tRNA from the A (1st) site to the P (2nd) site; makes room for new tRNA to bind and attach another amino acid
  32. Polyribosome
    multiple initiation events that usually take place on each mRNA being translated; ribosomes can be spaced as close as 80 nucleotides apart along a single mRNA
  33. formation of each peptide bond requires considerable:
    • ENERGY
    • • two high-energy bonds are used each cycle (EF-1 and EF-2)
    • • two high-energy phosphates are used to generate each aminoacyl-tRNA
  34. Where is the termination codon located in the mRNA?
  35. termination (release) factor
    • binds to the A site and promotes the cleavage of the polypeptide chain from the tRNA in the P site
    • • there are no tRNAs with anti-codons complementary to these sequences; elongation stops when one of these triplets appears opposite the A site on the ribosome
    • • this is followed by the release of the ribosome from the mRNA;
  36. What is monocistronic mRNA?
    mRNA that will code for only one polypeptide sequence. With very few exceptions, eukaryotic mRNA is monocistronic. Bacteria, on the other hand, frequently have polycistronic messages.
  37. In bacteria, the region of the 3' terminus of the 16S ribosomal RNA is complementary to the _______ (which sequence)
    Shine-Dalgarno Sequence; This is the ribosome binding site on the mRNA. In eukaryotes the equivalent sequence is known as the Kozak sequence.
  38. What is a missense mutation?
    A single base substitution in which one amino acid replaces another
  39. What is a nonsense mutation?
    A change in a codon that converts it to a stop codon, leading to premature termination of translation
  40. Effects of base substitutions on translation:
    • • cryptic splice site generation (can create or remove an exon)
    • • generation of termination signal
    • • loss of termination signal
    • • frame-shift mutations: can change the entire mRNA sequence and how it's supposed to be read
  41. What is a frameshift mutation?
    A mutation that causes the codons to be read out of frame, thereby leading to a misinterpretation of mRNA
  42. What is the sedimentation coefficient of bacterial ribosomes?
  43. What is translation?
    The process by which an mRNA template is used to synthesize a polypeptide chain
  44. What kind of bond links the carboxyl group of an amino acid to the 3' CCA sequence of a tRNA molecule?
    An ester bond
  45. What is an aminoacyl-tRNA?
    A tRNA molecule bound to its corresponding amino acid
  46. What is an anticodon?
    A tRNA trinucleotide sequence that is complementary, and therefore binds to, an mRNA codon
  47. What is the first tRNA that binds to the small ribosomal subunit?
    Met-tRNA (note that is binds regardless of whether or not there is a codon for methionine)
  48. Which initiation factor is required for the initiator tRNA (Met-tRNA) to bind to the small ribosomal subunit in eukaryotes?
    eIF2 (along with GTP)
  49. To which binding site does the initiator tRNA (Met-tRNA) bind to on the ribosome?
    It binds directly to the P site
  50. True or False: Interaction of the eIF2-GTP-Met-tRNA complex with the 40S ribosomal subunit must occur in the presence of mRNA?
    False, It typically occurs in the absence of mRNA
  51. What is the function of eIF2 during translation?
    It binds the 40S subunit to tRNA
  52. What happens to eIF2 when the anticodon of the initiator tRNA matches the AUG start codon?
    GTP is hydrolyzed, allowing eIF2 to dissociate from the ribosome and the 60S subunit to bind to the 40S subunit
  53. Which elongation factor is required for tRNA to bind to the A site of the ribosome?
  54. Which elongation factor is required for translocation of tRNA from the A site to the P site of the ribosome?
  55. Which enzyme is thought to catalyze the nucleophilic attack on the carbonyl group of the peptidyl-tRNA by the amino group of the aminoacyl-tRNA? Where does this reaction occur on the ribosome?
    The enzyme is peptidyl transferase and it occurs in the A site of the ribosome
  56. What is the function of the soluble protein called termination factor?
    It promotes the cleavage of the polypeptide chain from the tRNA in the P site, releasing the mRNA from the ribosome
  57. What is the shape of a typical tRNA?