Molecular Text 4.5

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  1. ·         Eukaryotes also contain a few __ that assemble into __, which are present in small amounts and are not as __
    ·         Major histones are made mostly during the __ and assembled into __ just behind the __. 
    • variant histones
    • nucleosomes
    • conserved
    • S phase of the cell cycle
    • nucleosomes on the daughter DNA helices
    • replication fork
  2. ·         In contrast, most histone variants are synthesized throughout __.
    o   They are often inserted into __, which requires a __ catalyzed by the __
    §  These __ contain subunits that cause them to do what? As a result, each histone variant is inserted into chromatin in a highly selective manner. 

    already-formed chromatin

    histone-exchange process

    ATP-dependent chromatin remodeling complexes

    remodeling complexes

    bind both to specific sites on chromatin and to histone chaperones that carry a particular variant
  3. ·         Thousands of modification combos can exist; and there is further diversity created by __that contain __. These combos have specific meaning because they determine what?
    • nucleosomes 
    • histone variants
    • how and when the DNA packaged in the nucleosomes is accesed, leading to the histone code hypothesis
  4. o   Small protein modules bind to specific marks, recognizing particular __. These module act in concert with other modules as part of a __, so as to allow particular combinations of markings on chromatin to do what? 
    • side hchains on histones
    • code-reader complex
    • attract additional protein complexes that execute an appropriate biological function at the right time.
  5. ·         The marks on nucleosomes due to __ are dynamic, being constantly removed and added at rates dependent on __
    o   Because the histone tails extend outward from the __ and are likely to be accessible even in __, they would seem to provide a suitable format for creating marks in a form that can be readily altered as a cell’s needs change
    • covalent additions to histones
    • chromosome location
    • nucleosome core
    • condensed chromatin
  6. ·         __ requires that some modified forms of chromatin have the ability to __
    ·         The enzymes that modify (or remove modifications form) the histones in nucleosomes are part of __. They can initially be brought to a particular region of chromatin by one of the __
    • Position effect variegation
    • spread for substantial distances along a chromosomal DNA molecule
    • multisubunit complexes
    • sequence-specific DNA –binding proteins (gene regulatory proteins)
  7. o   But after a modifying enzyme __, events that resemble a chain reaction can ensue.
    §  The __ works in concert with a __ located in the same protein complex.
    §  The second proteoin contains a __ that recognizes the mark and binds tightly to the newly modified __, positioning its attached writer enzyme near an adjacent nucleosome
    • “writes” its mark on one or a few adjacent nucleosome
    • code-writer enzyme
    • code-reader protein
    • code-reader module
    • nucleosome
  8. ·         Through many such __, the __ can carry the __ along the DNA—spreading the mark in a hand-over-hand manner along the chromosome
    ·         Both __ are part of a protein complex that is likely to contain multiple __, and to require multiple marks on the nucleosome to spread
    o   Moreover, many of these __ also contain an __, and the reader, writer, and remodeling proteins work in concert to either __  or _as the reader moves progressively along the __
    • read-write cycles
    • reader protein
    • writer enzyme
    • readers and writers
    • readers and writers
    • reader-writer complexes
    • ATP-dependent chromatin remodeling protein
    • decondense or condense long stretches of chromatin
    • nucleosome-packaged DNA
  9. ·         What prevents a cacophony of confusing cross-talk between adjacent chromatin domains of different structure and function?

    o   The existence of specific DNA sequences that separate one chromatin domain from another—they are barrier sequence
  10. §  Ex: HS4 domain contains the __ from an adjacent region of silenced, condensed chromatin. If this sequence is deleted, the __ is what, which does what, and it spreads to a different extent in different cells, causing a pattern of __
    ·         This invasion has dire consequences: the globin genes are poorly expressed, and individuals who carry such a deletion have a severe form of anemia
    • beta-globin locus
    • beta-globin locus
    • invaded by condensed chromatin
    • silences the genes it cover
    • position effect variegation
  11. ·         The __ is often added to both ends of a gene that is inserted into a mammalian genome to do what?
    o   It contains a cluster of __ for __
    §  Since the __ is incompatible with the __, histone acetylases and deacetylases are logical for formation of __
    ·         Several other types of chromatin modifications can also protect genes from silencing
    • HS4 sequence
    • protect that gene from silencing caused by spreading heterochromatin
    • binding site
    • histone acetylase enzymes
    • acetylation of a lysine side chain
    • methylation of the same side chain
    • barriers on the DNA that block the spread of different forms of chromatin
  12. ·         The presence of nucleosome carrying histone variants produces __ that are __
    o   For example, each centromere is embedded in a stretch of special __ that persists throughout __, even though the __ occur only during mitosis. 
    • marks in chromatin that are unusually long lasting
    • centric heterochromatin
    • interphase
    • centromere-mediated movement of DNA
  13. §  This chromatin contains a __, known as __, plus additional proteins that __ and __
    • centromere-specific variant H3 histone
    • CENP-A
    • pack the nucleosomes into particularly dense arrangement
    • form the kinetochore, the special structure required for attachment of the mitotic spindle.
  14. ·         The __in more complex organisms are considerably larger in those in budding yeasts; and, they consist of short, repeated DNA sequences, known as__ in humans. The same repeat sequences are also found at other (__) positions on chromosomes, indicating that they are __
    New human centromeres (called __) have been observed to form spontaneously on __. Some of these new positions were originally __and lack __ altogether
    • centromeres 
    •  alpha satellite DNA
    • non-centromeric
    • not sufficient to direct centromere formation
    • neocentromeres
    • fragmented chromosomes
    • euchromatic 
    • alpha satellite DNA
  15. ·         Centromeres in complex organisms are defined by an __, instead of by a __
    o   The stretched chromosome fibers from centromeres have __, which allows the __ to fold so as to position the __ on the outside of the mitotic chromosome where they do what, which in turn do what?
    • assembly of protein
    • specific DNA sequence
    • two modified forms of chromatin
    • centric heterochromatin
    • CEMP-A-containing nucleosomes
    • bind the set of proteins that form the kinetochore plates
    • capture a group of microtubule from the mitotic spindle in order to partition the chromosomes accurately
  16. ·         It has been proposed that __ requires an initial seeding event, involving the formation of a specialized DNA-protein structure that contains __formed with the__
    o   In humans, this seeding event happens more readily on arrays of __ than on other DNA sequence
    • de novo centromere formation
    • nucleosomes
    •  CENP-A variant of histone H3
    • alpha satellite DNA
  17. §  The __ from each nucleosome on the parental DNA helix are directly inherited by the __ at a __
    ·         Once a set of __ has been assembled on a stretch of DNA, it is easy to understand how a __ could be generated in the same place on both daughter chromosomes following each round of cell division
    • H3-H4 tetramers
    • daughter DNA helices
    • replication fork
    • CENPA-containing nucleosomes
    • new centromere
  18. ·         The __ may provide an important evolutionary advantage. Chromosomes that evolve by breaking and rejoining events produce __.
    o   Both the __ and their ability to be __ may occasionally allow newly formed chromosomes to be __, thereby facilitating the process of __
    • plasticity of centromeres
    • chromosomes with two centromeres or no centromeres
    • inactivation of centromeres
    • activated de novo
    • maintained stably
    • chromosome evolution
  19. ·         The formation and maintenance of centromeres is similar to the formation and maintenance of other regions of heterochromatin in that what?

    Moreover, once formed, the structure seems to be __
    the entire centromere forms as an all-or-none entity, suggesting a highly cooperative addition of proteins after a seeding event. 

    directly inherited on the DNA as part of each round of chromosome replication
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Molecular Text 4.5
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