Ch 6A Notes

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Ch 6A Notes
2015-02-23 11:08:09
Test Two
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  1. What is the central dogma?
    DNA (replication, repair, recombination) --> RNA (transcription)--> protein
  2. WHow can genes be controoled?
    • they can be expressed in different efficiencies
    • - can control amount of proteins produced via the amount of RNA

    can also affect timing of transcriptional, affecting development
  3. RNA molecules can __ since they are __. 

    This is done through __. 

    RNA was probably what?
    form 3D structures that are sequence determined

    internal hydrogen bonding between complemnetary sequences; fold into distinct shapes

    the first macromolecule that later got copied into DNA and became translated
  4. What are the steps for transcription? Briefly.
    • 1) Peel apart the DNA, exposing bases
    • 2) Pick correct strand to ensure we get the right sequence
    • 3) Transcribe RNA and separate it from teh template
    • 4) Reform the Hydrogen bonds in DNA
  5. RNA polymerase
    DNA-dependent RNA polymerase: uses DNA template to create an RNA polmyer
  6. Ribonucleoside triphosphate uptake channel
    building blocks are channeled directly into this active site
  7. True or False:
    A three prime hydroxyl group is needed for RNA polymerase?
  8. What else is contained in RNA polymerase?
    divalent cation, usually, Mg
  9. What drives the addition of ribonucleoside triphosphates
    the energy stored int heir phosphate phosphate bonds provides the driving force
  10. Bacterial RNA polymerase has __. 

    What is the domain structure?
    four subunits

    double-psi barrel, which forms the core of the polymerases
  11. double-psi barrel
    • protien domain that forms core of RNA polymerases
    • incldues dimerization of domain, insertion of large polypeptide "loops," the acquisition of two critical lysines and three aspartic acids
  12. Explain upstream and downstream.
    anything to the right of the promoter is downstream; anything to the left is upstream
  13. In order for transcirption to start, what must happen?
    • sequences must be recognized in the promoter sequence upstream of the transcription region:
    • TATA box centered around -10 in prok. and -25 in euk.
    • consensus sequence that is TTGACA, centered around -35 in pro and -75 in euk.
  14. Aside from the TATA box and the consensus sequence, what are the other sequences?
    enhancer sequences: located anywhere such as in introns; allows proteins to come and facilitate the start of the transcription
  15. Why are there two sequences?
    • sigma factor may hond on longer
    • gives direction to transcription; lets it know to transcribe downstream
  16. What is the transcription cycle of bacterial RNA polymerase?
    • 1) The RNA polymerase holoenzyme assembles and then locates a promoter. The sigma factor binds to the two binding sites. It hydrogen bonds.
    • 2) The polymerase unwinds the DNA (sigma factor helps melting of DNA) at the position at which transcription is to begin
    • 3) Transcription begins. The initial RNA synthesis (abortive initiation) is relatively inefficient. However, once RNA polymersae manages to make 10 nucleotides of RNA, it breaks its interactions with the promoter DNA and weakens, and breaks, its interaction with the sigma factor. 
    • 4) The polymerase now shifts to the elongation mode of RNA synthesis, moving rightward along the DNA
    • 5-6) During elongation, transcription is highly processive, with the polymerase leaving the DNA template and releasing the newly transcribed RNA when it encounters a termination signal.
    • 7) The termination signal destabilizes the polymerase's hold on the RNA by forming a hairpin structure
  17. RNA polymerase holoenzyme
    polymerase core enzyme plus sigma factor
  18. abortive initiation
    initial RNA synthesis that occurs before the elongation stage; inefficient

    RNA polymerase is not fully committed to transcribing gene

    at first 10 nucleotides due to confirmation
  19. termination signals
    typically encoded in DNA; funciton by forming an RNA structure that destabilizes the polymeras's hold on the RNA
  20. After abortive initiation, what occurs to allow elongation to proceed (in prokaryotes)?
    Rutter goes up, prying transcript off template

    sigma factor dislodges; full scale transcription mode
  21. Why does formation of the hairpin structure allow dislodging?
    There is less energy to overcome in the hydrogen bonds.

    The hairpin forms when the transcript lops around to form a hairpin structure, opening the rudding and sloing transcription. There are several GC pairs.