Chapter 11

  1. Chromatin is __, the latter including.
    the complex of DNA and protein

    regulatory (transcription), replicative, and histones
  2. Why is the conservation of histones so great?
    It shows the importance of the histones and the importance of their function. They are made of mostly basic amino acids.
  3. chromatosome
    • includes histone H1
    • complex of proteins
  4. Explain the 30 nm fiber
    Beads on a string allow the 6x compaction

    30-nm fiber allow the 7x compaction

    Packages the nucleosomes together. 

    It is the common structure in euchromatin, an actively transcribed region
  5. What is the organization of euchromatin in the nucleus?
    Loops of DNA organized in th 30-nm fiber are looped and anchored to the nuclear matrix. 

    Nuclear matrix may be analogous to the cell cytoskeleton

    Attachment of DNA via AT-rich segments: MARS and SARS

    Possible function for junk DNA
  6. Compact structures beyond the 30-nm fiber?
    heterochromatin: trnscriptional inactive regions
  7. What are the locations of the centromere?
    • metacentric: in the center
    • submetacentric: a little off center
    • acrocentric: more towards the end
    • telocentric: at the end
  8. What is the centromere composed of?
    repetitive DNA--> alphoid DNA (171 bp repeat)

    CENP-A instead of H3, allowing more rigidity, which is thought to be positioned on the outside of the centromere and serves as a platform for kinetochore assembly
  9. Spectral karyotype
    construction of chromosome specific fluorescently labeled dyes

    hybridization to metaphase spread

    individual metaphase are specifically "painted" a different fluorescent color
  10. What is the 5'- G-rich strand overhang sequence?
  11. What is the 3'-C -rich strand overhang sequence?
  12. What else do telomeres contain?
    • TRF1 (regulates length) 
    • TRF2 (protects overhang)
  13. Which telomere strand gets overhung?
  14. D-loop for telomeres
    a DNA structure where the two strands of a double-stranded DNA molecule are separated for a stretch and held apart by a third strand of DNA
  15. Shortening of telomeres leads to?
    replicative sensence

    cells no longer divide
  16. What are G1/S phase checkpoints?
    it is the start checkpoint. Is the environment favorable?

    ex: Wnt present; cell commits to replicating DNA and going all the way through the cycle; autopilot

    Also, is DNA damaged
  17. Most of the other checkpoints after G1 are ?

    • - has DNA been replicated correctly (inhibits S-phase transition)
    • - are they lined up
    • - are there broken or mismatch chromosomes
  18. What is the G2/M phase checkpoint?
    internal checkpoint: is all DNA replicated

    Is environment favorable
  19. What is the M phase checkpont?
    metaphase-to-anaphase transition

    trigger anaphase and proceed to cytokinesis

    are all chromosomes attached to the spindle?
  20. Cell cycle checkpoints are regulated by __ and __. How?
    cyclins and Cdks

    cyclins bind to Cdk
  21. What is the downside to telomerase?
    Telomerase expression is shut down in somatic cells. If you had a cell that is lost, for example, APC, it will proliferate more, creating a selective evolutionary pressure to express telomerase. It will have increased fitness compared to cells in the neighborhood
  22. What are cell cycle checkpoints?
    a set of criteria that need to be satisfied in order for cell transition to the next phase of the cell cycle
  23. There are specific combos of __ and __, which are required for each of the __. The transcription of __ and __ is important. 

    It is the function of the __ that puhes it along.
    • cyclins
    • corresponding CDKs


    CDKs and cyclins

    Cdk complex
  24. Where does each Cdk work?
    G1/ S- Cdk--> allows movement into S phase and production of S-cyclin

    S-Cdk--> allows DNA replication

    M-Cdk-- allows movement into the M phase

    APC/C: anaphase - promoting complex that allows anaphase to proceed
  25. Explain the rise and fall of cyclins.
    accumulation allows them to allow the transition tooccur
  26. Regulation of Cdks
    activation via phosphorylation by Cdk-activating kinase (CAK). The T-loop is phosphorylated

    inactivation by phosphorylation. There is another phosphate added that is an inhibitory phosphate. p27 attaches to form the p27-cyclin-Cdk complex
  27. T-loop of telomerase
    A t-loop is formed when the single-stranded 3' strand is looped back and anneals to the double-stranded hexamer repeats; as the G- rich strand displaces one strand a D, or displacement loop, is created
  28. What are other cycle cell regulations?
    • tyrosine kinase receptors
    • G protein coupled receptors
    • integrins
    • etc.
  29. Timing of replicatoin firing?
    regions of active gene expression are transcribed first
  30. Cyclins and Cdc6p
    cyclin activates it, which activates MCM helicase, which unwinds the helix at the origin of replication.
  31. One of the functions of cyclins and Cdks is __
    opening up the DNA, which occurs at origins of replication. They exist, but are quiet until the G1/S phase transition, where they will fire.
  32. In G1, what happens specifically?
    Cdc6P accumulates and binds to the origin of replication, calling MCM helicase.
  33. What is the protein that chops cohesin proteins in half?
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Chapter 11