Ch 6B Notes

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  1. What has to be correct?
    • The right strand
    • the correct reading frame
    • 3 potential reading frames for every segment of DNA
  2. Reading frame
    • the way the nucleotides are read from 5' to 3'
    • the same RNA sequence can specify three completely different amino acid sequences, depending on the reading frame. But, only one contains the actual message
  3. wobble
    tRNA is constructed so that they require accurate base pairing only at the first two positions of the codon and can tolerate a mismatch at the third position
  4. The carboxyl end of the amino acid forms an __ to ribose. Because the hydrolysis of this ester bond is associated with a large favorable change in free energy, the amino acid is said to be __.
    ester bond

  5. The genetic code is translated by means of two adaptors that act one after another. What are these two decoders?
    The initial check is via the aminoacyl-tRA synthetase, which couples a particular amino acid to its corresponding tRNA

    THe second is the tRNA molecule itself, whose anticodon forms base pairs with the apprpriate codon on the mRNA
  6. Aside from the decoders, what is the editing that takes place?
    Through hydrolytic editing of incorrectly attached amino acids, the correct amino acid is rejected by the editing site
  7. +Which rRNA is in the small subunit?
    • 18S in euk
    • 16S in pro
  8. What are the functions of the subunits?
    • large: forms peptidyl bond
    • small: grabs onto mRNA
  9. What does translocation of the large subunit do?
    causes hybrid sites to form
  10. Explain EF-Tu.
    it is a triple check system to ensure the correct amino acid is being added

    1)Introduces a slight delay to the process
  11. How are the elongation factors efficient?
    Coupling the GTP hydrolysis-driven changes in the elongation factors to transitions between different states of the ribosome speeds up protein synthesis

    Specifically, EF-Tu binds GTP and aminoacyl-tRNAs simultaneously.
  12. What is the specific mechanism of EF-Tu?
    The dissociation of the inorganic phosphate group, which follows the reaction GTPàGDP and Pi causes a shift of a few tenths of a nanometer at the GTP-binding site

    b. This tiny movement causes a conformational change to propagate along a crucial piece of alpha helix, called the switch helix, in the Ras-like domain of the protein.

    c. The switch helix seems to serve as a latch that adheres to a specific site in another domain of the molecule, holding the protien in a “shut” conformation.d

    . The conformational change triggered by GTP hydrolysis causes the switch helix to detach, allowing separate domains of the protein to swing apart, through a distance of about 4 nm.e. This releases the bound tRNA molecule, allowing its attached amino acid to be used.
  13. How do we start translation?
    • We ned key elements:
    • - mRNA with 5' cap and poly-A tail
    • - initiation complex: small ribosomal subunit/ initiator tRNA

    initiator tRNA moves along RNA, searching for the first AUG

    the initiator tRNA is bound to an eIF2 with GTP bound. The GTP and eIF2 dissociate once AUG is found
  14. Explain the formation of selenocysteine?
    a specialized tRNA is charged with serine by the normal seryl-tRNA synthetase, and the serine is subsequently converted enzymatically to selenocysteine.

    A specific RNA structure in the mRNA (a stem and lop structure with a specific nucleotide sequence) signals that selenocysteine is to be inserted at the neighboring UGA codon

    This requires the participation of a selenocysteine-specific translation factor
  15. What does the enzyme junction complex do?
    it binds to newly formed backbone at an exon exon junction

    mRNA, as it exits the nucleus, is test translated, removing EJCs from the mRNA
  16. What does incorrect splicing cause? 
    What helps this?
    it causes a pre-mRNA to introduce a premature stop codon into the reading frame for the protein

    nonsense-mediated mRNA decay: it destroys the abnormal mRNAs

    if an in-frame stop codon is encountered before the final exon junction complex is reached, the mRNA undergoes nonsense-mediated decay, which is triggered by Upf proteins that bind to each EJC
  17. What is the structure of a molten globule
    it is more open and less highly ordered than the final folded form of the protein

    the molten globule contains most of the secondary structure of the final form
  18. How can Hsp proteins detect improper folding?
    they detect improper folding because of their exposed hydrophobic regions
  19. Hsp70
    act early, recognizing hydrophobic amino acids on a protein's surface

    Aided by Hsp40 proteins, ATP-bound Hsp70 molecules grasp their target protein and hydrolyze ATP to ADp, undergoing conformational changes that cause the Hsp70 molecules to associate even more tightly with the target. 

    Rapid rebinding of ATP indues dissociation of the Hsp70
  20. Hsp60
    misfolded protein captured

    subsequent binding of ATP plus a protein cap increases the diameter of the barrel rim, which may stretch the client protein and confines it to an enclosed space

    ATP hydolysis then occurs--> weakens complex

    ATP binding then ejects the protein and the cycle repeats
  21. What tag is recognized by proteasomes?
    tagged with a 76 amino acid tag called ubiquitin, which is attached to specific regions of proteins or subunits called degroms, which contain a lysine
  22. unfoldase
    proteins that make up the ring structure in the proteasome cap belong to this class of unfoldases called AAA proteins'

    six subunits with ATP binding sites

    causes shuttling in of substrate
  23. Ub-ligase
    3 component enzyme system

    E1: Ub activating protein (generic finds Ub in cell, grabs ATP and uses ATP)

    E2 and E3 are more specific; have to recognize different degrons

    E2: Ub conjugating protein (transfers to a cysteine residue in E2)

    E3: Ub ligase, but doesnt work without E2
  24. E3
    has to be complementary

    once bound, E2 transfers Ub to lysine residue and target protein

    degron binds to binding site in E3
  25. Activation f a Ubiquitin ligase
    1) phosphorylation by protein kinase (In E2-P= off/ in E3-P= off)

    2) allosteric transition caused by ligand binding 

    3) allosteric transition caused by protein subunit addition
  26. Activation of a degradation signal
    • protein subunit blocks degron
    • Phosphorylation by protein kinase

    unmasking by protein dissociation

    creation of destabilizing N-terminus
  27. What is the easiest stage to control protein formation?
    the transcription level, but there are also other checks
Card Set
Ch 6B Notes
Test Two
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