Chapter 6B ID Terms

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Chapter 6B ID Terms
2015-02-17 12:11:46
Test Two
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  1. polynucleotides
    Can directly guide the formation of copies of their own sequence, depending on the complementary base pairing of nucleotide subunits, which enables one polynucleotide to act as a template for the formation of another
  2. peptide synthetase enzymes
    Assemble short peptides, without mRNAs guiding their synthesis
  3. genetic code
    The code by which the nucleotide sequence is converted into the amino acid sequence; there are 64 combos of three nucleotides
  4. codon
    Each group of three consecutive nucleottides in RNA; each specifies either one amino acid or a stop to the translation process
  5. Reading frames
    An RNA sequence can be translated in any one of three different of these; only one of three encodes the required protien
  6. tRNAs
    Structure: four short segments; resembles a cloverleaf; has an anticodon and an amino end; L-shapedFunction: carries the appropriate amino acid encoded by the anticodon; each tRNA is specific for the amino acid it carries
  7. anticodon
    A set of three consecutive nucleotides that pairs with the complementary codon in an mRNA molecule
  8. ribozymes
    RNA molecules that possess catalytic activity
  9. initiator RNA
    Carries methioine and starts translation; has a nucleotide sequence distinct from that of the tRNA that normally carries methionine; it’s the only tRNA capable of tightly binding the small ribosome subunit without the complete ribosome being present and it binds directly to the P-site
  10. polycistronic
    Encoding several different proteins, each of which is translated from the same mRNA
  11. molecular mimicry
    Release factors are an example of this; one type of macromolecule resembles the shape of a chemically unrelated molecule; the 3D structure of the release factors resembles the shape and charge distribution of a tRNA, helping them enter the A site on the ribosome and cause translation termination
  12. teflon coating
    Coating of the walls of the water-filled tunnel in the large subunit of the ribosome that the polypeptide goes through; walls are made of 23S rRNA and are tiny hydrophobic surfaces embedded in hydrophilic surfaces
  13. polyribosomes
    Large cytoplasmic assemblies made up of several ribosomes spaced as close as 80 nucleotides apart along a single mRNA molecule, allowing multiple translations of the same mRNA
  14. translation recoding
    Other nucleotide sequence information present in an mRNA can change the meaning of the genetic code at a particular site in the mRNA molecule
  15. selenocysteine
    Enzymatically produced from a serine attached to a special tRNA molecule that base-pairs with the UGA codon, a codon normally used to signal a translation stopThe mRNAs for proteins in which selenocysteine is to be inserted at a UGA codon carry an additional nucleotide sequence in the mRNA nearby that causes the recoding event
  16. translational frameshifting
    Allows more than one protein to be synthesized from a single mRNA; retroviruses use it to make capsid proteins (Gag)  and viral reverse transcriptase and integrase (Pol proteins) from the same RNA transcript
  17. nonsense-mediated mRNA decay
    • Brought into play when the cell determines that an mRNA has a nonsense codon in the wrong place
    • Eliminates defective mRNAs before they can be efficiently translated into protein
  18. molten globule
    The unusually dynamic and flexible state of a compact structure containing mostly secondary features after the polypeptide chain emerges from the ribosome
  19. molecular chaperones
    Help proteins fold; uses ATP hydrolysis to perform mechanical work and also to ensure that protein folding is accurate; they can recognize misfolds, halt further misfolding, and recommence folding in an orderly way
  20. Heat-shock proteins (Hsp)
    They are synthesized in increased amounts after brief exposure of cells to elevated temperatues; reflects the operation of a feedback system that responds to an increase in misfolded proteins by boosting the synthesis of the chaperones that help these proteins refold

    Hsp60 and Hsp70 proteins work with their own small set of associated proteins when they help other proteins to fold

    They share an affinity for the exposed hydrophobic patches on incompletely folded proteins, and they hydrolyze ATP, often binding and releasing their protein substrate with each ATP hydrolytic cycle
  21. Hsp70
    Acts early in the life of many proteins, binding to a string of about seven hydrophobic amino acids before the protein leaves the ribsome
  22. Hsp60
    Forms a large barrel-shaped structure that acts after a protein has been fully synthesized; called a chaperonin, it forms an isolation chamber into which misfolded proteins are fed, preventing their aggregation and providing them with a favorable environment in which to attempt to refold
  23. Proteasome structure
    Structure: central hollow cylinder formed from multiple protein subunits that assemble as a quasi-cylindrical stack of four heptameric rings; some subunits are distinct proteases whose active sites face the cylinder’s inner chamber; the design prevents these highly efficient proteases from running rampant through the cell

    • Each end of the cylinder is associated with a
    • large protein complex (the 19S cap), which contains a six-subunit protein ring,
    • through which target proteins are threaded into the proteasome core where they
    • are degraded
  24. proteasome
    An abundant ATP-dependent protease that constitutes nearly 1% of cell protein; destroys aberrant proteins o the ER, which are detected by ER-based surveillance systems that detect proteins that fail to fold or be assembled properly, and retrotranslocates them back to the cytosol for degradation
  25. AAA proteins
    the proteins that make up the ring strucute in the proteasome cap belong to a class of protein unfoldases called this; many function as hexamers
  26. ubiquitin
    • Recognition tag that exists in cells either free or covalently linked to many different intracellular proteins; tagging by it results in their destruction by the proteasome
    • The number of ubiquitin molecules added and the way they are linked determines how the cell interprets the message
  27. ATP ubiquitin-activating enzyme (E1)
    Creates an activated, E1-bound ubiquitin that is transferred to ne of a set of ubiquitin-conjugating (E2) enzymes, which act in conjuction with accessory (E3) proteins
  28. Ubiquitin ligase
    The E2-E3complex; the E3 component binds to specific degradation signals, called degrons, in protein substrates, helping E2 to form a polyubiqutin chain linked to a lysine of the substrate protein; in this chain, the C-terminal residue of each ubiquitin is linked to a specific lysine of the preceding ubiquitin molecule, producing a linear series of ubiquitin-ubiquitin conjugates

    Distinct ubiquitin ligases recognize different degradation signals and therefore target distinct subsets of intracellular proteins for destruction