Molecular Text 4.7

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Molecular Text 4.7
2015-01-25 16:04:40
Test One
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  1. ·         The __is the largest subcompartment. Nucleolar regions consist of networks of __surrounding __, often existing as multiple __
    o   The __is the cell’s site of __, as well as the place where many other specialized reactions occur
    • nucleolus 
    • RNA and protein 
    • transcribing ribosomal RNA genes
    • nucleoli
    • nucleolus 
    • ribosome assembly and maturation
  2. ·         Inside the nucleus are also __ and __, which are composed of __ and __ that bind together to create networks that are highly __ to other protein and RNA molecules in the surrounding __ 
    o   Structures such as these can create distinct biochemical environment by doing what, as can other networks of __ and __ associated with __ and with the __. 
    • Cajal bodies
    • interchromatin granule clusters
    • selected protein and RNA molecules
    • permeable 
    • nucleoplasm
    • immobilizing select groups of macromolecule
    • proteins and RNA molecules
    • nuclear pores
    • nuclear envelope
  3. §  In principle, this allows the molecules that enter these spaces to be __.
    ·         Highly permeable, fibrous networks of this sort can thereby impart many of the kinetic advantages of __to reactions that take place in the nucleus 
    • processed with great efficiency through complex reaction pathways
    • compartmentalization
  4. ·         However, unlike the membrane-bound compartments in the cytoplasm, these nuclear subcompartments—__—can neither __
    ·         The cell can construct __ inside the nucleus.
    o   Like the nucleolus, these subcompartments appear to__, and they create a __ 
    • lacking a lipid bilayer membrane
    • concentrate nor exclude /specific small molecules
    • distinct biochemical environments

    •  form only as needed
    • high local concentration of the many different enzymes and RNA molecule needed for a particular process
  5. §  When DNA is damaged by ___, the set of enzymes needed to carry out DNA repair are observed to __, creating “__”
    ·         And nuclei often contain hundreds of __ for DNA or RNA synthesis
    • irradiation
    • congregate in discrete foci inside the nucleus
    • repair factories
    • discrete foci representing factories
  6. ·         Tethers are used to __
    ·         The nuclear matrix, or scaffold, has been defined as the __
    help to speed biological processes in the cytoplasm, increasing specific reaction rates

    insoluble material left in the nucleus after a series of biochemical extraction steps
  7. ·         Many of the proteins and RNA molecules that form this __ are likely to be derived from the __, while others seem to be proteins that help to __ or to __
    o   Whether or not the nucleus also contain long filaments that form organized tracks on which nuclear components can move is till disputed
    • insoluble material
    • fibrous subcompartments of the nucleus
    • form the base of chromosomal loops
    • attach chromosomes to other structures in the nucleus
  8. ·         Condensation of chromosomes during mitosis does what, but changes chromosome appearance
    o   The mitotic chromosome at the metaphase stage of mitosis contains __ and covered with a variety of molecules, including large amounts of RNA-protein complexes. 
    • reduces the length of the typical interphase chromosome only about tenfold
    • two sister chromatids held together at their centromeres
  9. ·         The order of visible features along a mitotic chromosome roughly reflects the __
    o   Mitotic chromosome condensation can be thought of as the __ 
    • order of genes along the DNA molecule
    • final level in the hierarchy of chromosome packaging
  10. ·         The compaction of chromosomes during mitois is a highly organized and dynamic process that serves at least two important purposes
    o   First, ???
    §  Thus, the sister chromatids can __ when the __ begins pulling them apart

    when condensation is complete (in metaphase), sister chromatids have been disentangled from each other and lie side by side.

    • easily separate
    • mitotic apparatus
  11. ·         The compaction of chromosomes during mitois is a highly organized and dynamic process that serves at least two important purposes

    o   Second, the compaction of chromosome protect the relatively fragile DNA molecules from being broken as they are pulled to separate daughter cells
  12. ·         The condensation of interphase chromosomes into mitotic chromosomes begins in early__, and it is intimately connected with the progression of the __.
    o   During M phase, __ shuts down, and specific modifications are made to __that help to __
    • M phase
    • cell cycle
    • gene expression
    • histones 
    • reorganize the chromatin as it compacts
  13. §  The compaction is aided by a class of proteins, called __that use the energy of __ to help __to produce the __ of a mitotic chromosome

    • condensins 
    • ATP hydrolysis
    • coil the two DNA molecules in an interphase chromosome 
    • two chromatids
  14. ·         Condensins are __; these dimers form when __
    o   When added to purified DNA, condensins can make large __in DNA molecules in a reaction that requires ATP
    • large protein complexes built from SMC protein dimers
    • two stiff, elongated protein monomers join at their tails to form a hinge, leaving two globular head domains at the other end that bind DNA and hydrolyze ATP
    • right-handed loops
  15. ·         Condensins are a major structural component that end up at the core of __, with about one molecule of condensing for every 10,000 nucleotides of DNA
    o   When condensins are experimentally depleted from a cell, __ still occurs, but the process is abnormal
    • metaphase chromosomes
    • chromosome condensation
  16. ·         The actual nucleotide sequences of many gene are sufficiently well conserved that homologous genes--__—can often be recognized across vast __distances
    ·         The recognition of __ has become a major tool for inferring gene and protein function ; it is possible to predict the __ in human for which no biochemical or genetic information is available simply by comparing their nucleotide sequences with the sequences of genes in other organisms 
    • genes that are similar in both their nucleotide sequence and function because of a common ancestry
    • phylogenetic 
    • sequence similarity
    • function of gene
  17. ·         __ are more tightly conserved than is overall __ 
    ·         The number of genes is only very roughly correlated with the __
    o   Much of the increase in gene number observed with increasing biological complexity involves the __, an observation that establishes gene duplication and divergence as major evolutionary processes
    • Gene sequences
    • genome structure
    • phenotypic complexity of an organism
    • expansion of families of closely related genes
  18. ·         Cells in the germline don’t have specialized mechanisms for creating changes in the structures of their genomes: evolution depends instead on __ and __ followed by __
    o   Most genetic changes result from __in the normal mechanisms by which genomes are copied or repaired when damaged, although the movement of __ elements also plays an important role
    o   Mechanisms for maintaining DNA sequences are precise, but are not perfect
    • accidents and mistakes followed by nonrandom survival
    • failures
    • transposable DNA
  19. ·         Errors in DNA replication, DNA recombination, or DNA repair can lead either to simple changes in DNA sequence—such as the __—or to large-scale genome rearrangements such as __(4)__ from one chromosome to another

    • substitution of one base pair for another
    • deletions, duplicatons, inversions, and translocations of DNA
  20. Various __ are an important source of genomic change
    o   These __are __ that __
    §  In the process, they often __
    • mobile DNA elements
    • transposable DNA elements (transposons) 
    • parasitic DNA sequences
    • colonize genomes and can spread within them
    • disrupt the function or alter the regulation of existing genes
  21. ·         On occasion, they even create altogether novel genes through __
    o   Over evolutionary time, __have affected the structure of genomes
    §  In fact, nearly half of the DNA in the human genome has recognizable sequence similarity with known __sequences, thereby indicating that these sequences are remnants of past transposition events 
    • fusions between transposon sequences and segments of existing genes
    • transposons 
    • transposon
  22. ·         Differences have accumulated
    ·         Comparing genomes is through __, which compares gene or protein sequences
    ·         For closely related organisms, its easy to __ of the extinct, last common ancestor of the two species
    ·         Even DNA sequences whose nucleotide order is functionally unconstrained are nearly identical in humans and chimps
    • phylogenetic trees
    • reconstruct the gene sequence
  23. ·         For less closely related organisms, the sequence conservation found in genes is due to __, rather than to an inadequate time for mutation to occur.
    o   __(3)__ in the DNA are often remarkably conserved
    o   In contrast, most DNA sequences in the human and chicken genomes have diverged so far due to multiple mutations that make it impossible to align 
    • purifying selection (selection that eliminates individuals carrying mutations that interfere with important genetic functions)
    • Protein-coding, RNA-coding, and regulatory sequence