Ch 6 Notes AB

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Ch 6 Notes AB
2015-02-25 23:49:14
Test Two
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  1. RNA pol 1
    5.8, 18, and 28S rRNA
  2. RNA pol II
  3. RNA pol III
    tRNA, 5S rRNA
  4. Which general TF binds first?

    it contains a TBP subunit taht specifically recognizes the TATA sequence on the promoter

    it causes bending of the DNA
  5. CTD
    carboxy-terminal domain

    tail of polypeptide with lots of serines that get phosphorylated; unique to RNA pol II
  6. What is another important general TF?

    uses ATP to act as a helicase; also a kinase involved in phosphorylation of serine residues in CTD
  7. After CTD region is phosphorylated, what occrs?
    conformational change that allows the rudder to peel off and TFs to dissociate
  8. How does the mediator work?
    it randomly bumps into and binds other components of the complex. It will then bind the promoter sequence to allow transcription to start
  9. How can ribosomes distinguish between mRNA ffrom others?
    • 5' cap
    • poly-A-tail
  10. A single transcript can do what? 

    What flanks the coding sequence?
    make several mRNA sequences

  11. What are the steps for capping?
    • 1) remove a phosphate: 3 P--> 2 P
    • 2) get GTP and use the energy associated with removal of two phosphates and attach the one phosphate to the end of a nascent message
    • 3) add a methyl group to the G residue--> ending up with a 7-methylguanosine
  12. What is alternative splicing and what does it do?
    coming up with alternate ways of splicing; picking and choosing which exons are used gives proteins different functions
  13. Where are beginning and ends of introns and exons?
    People identified small consensus sequences common to particular function at exon-intron boundaries

    Nucleotide sequence IDed as binding sites for RNA and proteins
  14. How is the adenine nucleotide found?
    • In two ways:
    • - initially, A is recognized by the brotein BBP (branch point) in formation of the lariat
    • - protein has a site that specifically recognizes nucleotide
  15. What is the process of splicing with the snRNAs/
    1) The Adenine is identified b BBP, which recognizes it. 

    2) The BBP is replaced by other proteins that have RNA= snRNP; now A is recognized by RNA 

    3) U1 then binds to splice site after A is identified. More snRNPs are brought in and lasso begins to form

    4) Activated A brought to splice site; backbone is broken--> lasso forms, causing a conformational change, which brings the two exon ends together
  16. What makes the snRNAs able to perform their function?
    They base pair with RNA to position them appropriately

    the proteins hydrolyze ATP and undergo conformational changes that will move things around
  17. How is ATP used in splicing?
    to allow proteins to rearrange things; they also form a catalytic site
  18. What errors in splicing can occur?
    exon skipping: missing an exon

    crytic splicing: caused by nucleotide changes
  19. What helps to avoid problems in splicing?
    size of the exons and introns; average exon is around 150 bases long
  20. What is a disease caused by improper splicing?
    problems with splicing of beta-hemoglobin
  21. What is a hypothesis regarding hnRNP?
    • it is done during transcription
    • --> proteins immediately grab onto mRNA= SR protiens (Concentrated in serine and arginine residues); they bind to exons

    introns produced; large complexes with introns and protiens bunched together; allows snRNPs to better interact
  22. SR proteins
    have roles in alternative and constitutive splicing resulting in differential gene expression and also play a part in mRNA export, genome stabilization, non-sense mediated decay, and translation
  23. What are some ways in which beta thalassemia can be formed?
    exon skipping caused by nucleotide changes that destroy a normal splice site

    new exon incorporation by nucleotide chainges
  24. What do poly-A binding proteins do?
    bind to the poly-A tail that was made by PAP
  25. Explain the eIF factors?
    4E binds to the 5' cap

    4G binds to 3' poly A tail

    must be present in cytoplasm for translation
  26. CBC
    cap binding complex: binds to the 5' cap of pre-mRNA
  27. What signifies that the RNA is rRNA?
    a pseudouridine and 2'-O-methylated nucleotide
  28. What does a snoRNA do in the nucleolus?
    it works in conjunction with snoRNP; they determine the sites of modification by base pairing to complementary sequences on the precursor rRNA; bound to proteins, and the complexes are called snoRNPs, which contain both the guide sequences and the enzymes taht modify the rRNA
  29. What is the pre-mRNA splicing mechanism?
    The exchange of U1 snRNP for U6 snRNP occurs before the first transesterification; this exchange requires the 5' splice site to be read by two different snRNPs, thereby increasing the accuracy of 5' splice site to be read by two different snRNPs, thereby increasing the accuracy of the 5' splice site selection

    The branch point site is recognized by BBP and then U2; this check and recheck strategy provides icnreased accuracy of site selection. 

    U2 binds, forcing the appropriate adenine to be unpaired adn activated for the attack on the 5' splice site. 

    This, in combo with recognition by BBP is the way the spliceosome chooses the right adenine. 

    After the first transesterification, a series of rearrangements brings the two exons together for the second transesterification. 

    The snRNAs both position the reactants and provide the catalytic sites for the two reactions. 

    The U5 is present in the spliceosome before the rearrangement