Molecular Text 4.3

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Molecular Text 4.3
2015-01-25 13:47:06
Test One
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  1. ·         The proteins that bind to the DNA to form eukaryotic chromosomes are traditionally divided into two general classes: the __ and the __. The complex of both classes of proteins with the nuclear DNA of eukaryotic cells is __
    o   The total mass of histones in chromatin is about equal to that of __
    • histones and the nonhistone chromosomal proteins
    • chromatin
    • DNA
  2. ·        Histones are responsible for the __
    o   When __ are broken open very gently and their contents examined under the EM, most __is in the form of a fiber with a diameter of about 30 nm
    §  If partially unfolded, it looks like __, with the string being __and the beads being a __ that consists of DNA wound around a protein core formed from histones
    • first and most basic level of chromosome packing, the nucleosome, a protein DNA complex
    • interphase nuclei
    • chromatin 
    • bead on a string
    • DNA 
    • nucleosome core particle
  3. ·         Structural organization of __ was determined after first __ from __ by __ with particular enzymes (called __) that break down __ by __.
    o   After digestion for a short period, the exposed DNA between the nucleosome core particles, the __, is degraded.
    • nucleosome 
    • isolating them from unfolded chromatin by digestion
    • nucleases
    • DNA by cutting between the nucleosomes
    • linker DNA
  4. §  Each individual __ particle consists of a complex of __—two molecules each of histone, __(4)__—and __ that is 147 nucleotide pairs long.
    ·         The histone octamer forms a __ around which the double-stranded DNA is wound
    • nucleosome core
    • eight histone proteins
    • H2A, H2B, H3, and H4
    • double-stranded DNA
    • protein core
  5. ·         Each nucleosome core particle is separated from the next by a region of __, which can vary in length from a few nucleotide pairs up to about 80
    o   Nucleosome technically refers to a __, but it is often used synonymously with __
    • linker DNA
    • nucleosome core particle plus one of its adjacent DNA linkers
    • nucleosome core particle
  6. ·         Nucleosome repeat at interval of about __
    o   The formation of nucleosome converts a DNA molecule into a __ 
    • 200 nucleotide pairs
    • chromatin thread about one-third of its initial length
  7. ·         A nucleosome has a __ around which DNA is tightly wrapped in a __
    o   All four of the histones that make up the core of the __are relatively small proteins (102-135 amino acids), and they have a __, known as the __, formed from __ connected by __
    • disc-shaped histone core
    • left-handed coil
    • nucleosome 
    • structural motif
    • histone fold
    • three alpha helices connected by two loops
  8. §  In assembling a nucleosome, what happens?

    the histone folds first bind to each other to form H3-H4 and H2A-H2B dimer, and the H3-H4 dimers combine to form tetramers

    An H3-H4 tetramer then further combine with two H2A-H2B dimers to form the compact octamer core, around which the DNA is wound
  9. ·         The interface between __ and __ is extensive: __ are formed between __ and the __ in the __
    o   Nearly half of these bonds form between the __ and the __
    Numerous __ and __ also hold DNA and protein together in the __. These numerous interactions explain in part why DNA of virtually any sequence can be what?
    • DNA and histone
    • 142 hydrogen bonds
    • DNA and the histone core in each nucleosome
    • amino acid backbone of the histone
    • phosphodiester backbone of the DNA
    • hydrophobic interactions and salt linkages
    • nucleosome
    • bound on a histone octamer core
  10. ·         The path of the DNA around the histone core is __; rather, __ are seen in the DNA; and the bending requires a __
    o   Certain __in the __ are especially easy to compress, and some nucleotide sequences bind the __more tightly than others
    §  For most of the DNA sequence found in chromosomes, the sequence preference of nucleosome must be __ to allow __, inasmuch as nucleosomes can occupy any one of a number of positions relative to the DNA sequence in most chromosomal regions
    • not smooth
    • several kinks
    • substantial compression of the minor groove of the DNA helix
    • dinucleotide 
    • minor groove
    • nucleosome 
    • small enough
    • other factor to dominate
  11. ·         In addition to its histone fold, each of the core histones has an __, which extends out from the __.
    o   These histone tails are subject to __ that in turn control critical aspects of __ and __ 
    • N-terminal amino acid “tail”
    • DNA-histone core
    • several different types of covalent modifications
    • chromatin structure and function
  12. ·         The __are among the most highly conserved eukaryotic proteins, suggesting that the functions of __involve nearly all of their amino acids, so that a change in any position is deleterious to the cell
    o   Most changes in __ are lethal; the few that aren’t lethal cause changes in the normal pattern of __
    • histones 
    • histones 
    • histone sequences
    • gene expression
  13. ·         Despite the high conservation of the core histone, eukaryotic organisms also produce smaller amounts of __that differ in amino acid sequence from the main one. These variants, combined with a surprisingly large variety of __ that can be added to the __ in __, make possible the many different __ that are required for DNA function in higher eucaryotes. 
    • specialized variant core histones 
    • covalent modifications
    • histone in nucleosomes
    • chromatin structures
  14. ·         It was believed that nucleosomes do what because of the __. This would be bad since what?
    • remain fixed in place 
    • very tight association between its core histone and DNA
    • genetic readout mechanism require rapid access to many specific DNA sequence, as well as for the rapid passage of the DNA transcription and replication machinery through chromatin
  15. o   In actuality, DNA __from each end at rate of about 4 times per second, remaining exposed for 10 to 50 milliseconds before the__ __.
    §  Thus, most of the DNA in an isolated nucleosome is in principle __ 
    • unwraps 
    •  partially unwrapped structure recloses
    • available for binding other proteins
  16. ·         For the chromatin in a cell, a further __ is clearly required, because eukaryotic cells contain a large variety of__
    o   The subunits in these complexes that __ is evolutionarily related to the __, and it binds both to the __ and to the __
    • loosening of DNA-histone contacts
    • ATP-dependent chromatin remodeling complexes
    • hydrolyzes ATP
    • DNA helicases
    • protein core of the nucleosome
    • double-stranded DNA that winds around it
  17. §  By using the __ to move this DNA relative to the __, this subunit changes the structure of a __temporarily, making the DNA __. 
    ·         Through repeated cycles of ATP hydrolysis, the __ can catalyze __, and by pulling the __ along the DNA double helix in this way, they make the nucleosomal DNA available to other proteins in the cell 
    • energy of ATP hydrolysis
    • nucleosome 
    • less tightly bound to the histone core.
    • remodeling complexes
    • nucleosome sliding
    • nucleosome core
  18. o   In addition, by cooperating with __that serve as __, some remodeling complexes are able to do what—catalyzing either an __, or the complete __
    • negatively charged proteins 
    • histone chaperones
    • remove either all or part of the nucleosome core from a nucleosome
    • exchange of its H2A-H2B histone
    • removal of the octameric core from the DNA
  19. ·      Cells contain dozens of different __ that are specialized for different role. Most are large protein complexes that can contain 10 or more subunits.
    o   The activity of these complexes is controlled by __
    §  As gene are turned on and off, __ are brought to __ where they act __to __
    • ATP-dependent chromatin remodeling complexes
    • the cell
    • chromatin remodeling complexes
    • specific regions of DNA
    • locally 
    • influence chromatin structure
  20. ·         A __can occupy any one of a number of positions relative
    o   The most important influence on nucleosome positioning appears to be the __. Some bound proteins favor the formation of a __adjacent to them
    • nucleosome 
    • presence of other tightly bound proteins on the DNA
    • nucleosome
  21. §  Others create obstacles that force the nucleosome to __
    ·         The exact position of nucleosome along a stretch of DNA depends mainly on the __
    o   Due to the presence of __, the arrangement of nucleosome on DNA can be highly __, changing rapidly according to the needs of the cell
    • move to positions between them
    • presence and nature of other proteins bound to the DNA
    • ATP-dependent remodeling complexes
    • dynamic