Molecular Text 5.1

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  1. DNA replication is __ and must occur __. Maintaining order requires __ and __. While the short-term survival of a cell depend on __, the long-term survival of a species requires __
    the accurate duplication of vast quantities of genetic information carried in chemical form as DNA

    before a cell can produce two genetically identical daughter cell

    surveillance and repair

    preventing changes in its DNA

  2. a.       Permanent changes in DNA are __and can destroy organism if they occur at __
    b.      The __, the rate which observable changes occur in DNA sequences, can be determined from experiments.
    c.       __ can measure mutation rate. The fraction of amino acids that differ between any two species can be compared with the estimated number of years since that pair of species diverged from a common ancestor
    • mutations 
    • vital positions in the DNA sequence
    • mutation rate

    Comparing amino acid sequences of the same protein in several species
  3. a.       The sequence of one family of protein fragments does not seem to matter, allowing the genes that encode them to __.
    These are the __, fragments 20 amino acids long that are discarded when the __ is activated to form __during blood clotting
    accumulate mutations without being selected against


    protien fibrinogen

  4. a.       Germ cells __ and somatic cells __
                                                                  i.      Germ cells must __; and, somatic cells must be __
    1.       Nucleotide changes in somatic cells can give rise to __, some of which, through __, proliferate rapidly at the expense of the rest of the organism
    __: uncontrolled cell proliferation
    • transmit genetic information from parent to offspring
    • form the body of the organism
    • avoid mutation to maintain the species
    • protected to safeguard each indivudial
    • variant cells
    • natural selection
    • Cancer
  5. a.       Both for the __and for the __, multicellular organisms depend on the remarkably high fidelity which DNA sequences are replicated and maintained
    perpetuation of a species with a large number of genes (germ cell stability) 

    prevention of cancer resulting from mutations in somatic cells (somatic cell stability)
  6. a.       DNA templating is __
                                                                  i.      This process entails the __, as well as __
    the mechanism the cell uses to copy the nucleotide sequence of one DNA strand into a complementary DNA sequence

    recognition of each nucleotide in the DNA template strand by a free (unpolymerized) complementary nucleotide

    separation of the two strands, exposing hydrogen-bond donor and acceptor groups on each DNA base for base-pairing with the appropriate incoming free nucleotide
  7. a.       DNA polymerase is a __
    b.      DNA replication is __

    nucleotide-polymerizing enzyme that uses free nucleotides as substrates and a single-stranded DNA as the template

  8. First, at the __, a multienzyme complex that contains the __ synthesizes the DNA of both new daughter strands 
    replication fork (a Y-shaped structure that is a localized region of replication)

    DNA polymerase
  9. a.       Problem 1: __orientation requires synthesis in __ and the other in __, which would require two different types of __. However, it doe not.
                                                                  i.      Solution: __ syntheized in the 5’à3’ direction
    1.       Research: a __ was added to bacteria so the recently replicated DNA became radiolabeled
    • antiparallel 
    • 5-->3
    • 3-->5
    • DNA Polymerase

    Okazaki fragments (pieces of DNA that were 1000-2000 nucleotides long) 

    radioactive H-thymidine
  10.                                                               i.      A replication fork has an __, with a leading strand synthesized __and a lagging strand that is synthesized __
    1.       For the lagging strand, the direction of nucleotide polymerization is __; still done by __
                                                                ii.      Some changes that can occur in copying DNA can be: __ . They don’t change __
    • asymmetric structure
    • continuously 
    • discontinuously
    • opposite to the overall direction of DNA chain growth; still done by DNA polymerase

    • Two hydrogen bonds forming between G and T and rare tautomeric forms of the four DNA bases
    • helix geometry
  11. There are several proofreading mechanisms. 
    TRUE or FALSE?
  12.                                                               i.      __: first proofreading step before nucleotide addition
    1.       The correct nucleotide has a __ for the __ than does the incorrect nucleotide, because the correct pairing is more __
    a.       After nucleotide binding, but before the nucleotide is covalently added to the growing chain, the enzyme must __.
                                                                                                                                          i.      This change occurs more with correct base-pairing= __ 
    • DNA polymerase
    • higher affinity
    • moving polymerase
    • energetically favorable
    • undergo a conformational change in which its “fingers” tighten around the active site
    • double check
  13.                                                               i.      __: right after an incorrect nucleotide is covalently added to the growing chain
    1.       DNA polymerase enzymes only do what?
    a.       Those with a __ aren’t good templates and are not extended
    • Exonucleolytic proofreading
    • elongate specific DNA chains with a previously formed base-paired 3’-OH end of a primer strand
    • mismatched nucleotide at the 3’-OH end
  14. 1.       Solution: corrects this by means of a __

    separate catalytic site (either in a separate subunit or in a separate domain of the polymerase molecule, depending on the polymerase).
  15. a.       The 3’-to-5’ proofreading exonuclease does what until what?
                                                                ii.      In this way, DNA polymerase functions as a “__that removes its own __ as it moves along the DNA
    • clips off any unpaired residues at the primer terminus
    • enough nucleotides have been removed to regenerate a correctly base-paired 3’-OH terminus that can prime DNA synthesis
    • self-correcting” enzyme 
    • polymerization errors
  16. a.       The self-correcting properties of the __ depend on its requirement for a __, and it is apparently not possible for __
                                                                  i.      RNA polymerase don’t need efficient __: errors in why not?
                                                                ii.      RNA polymerases can start a new chain with__ 
    • DNA polymerase
    • perfectly base-paired primer terminus
    • such an enzyme to start synthesis anew
    • exonucleolytic proofreading mechanisms
    • making RNA are not passed on to the next generation, and the occasional defective RNA molecule that is produced has no long-term significance
    •  no primer
  17. a.       Why in the 5’à3’ direction only?
                                                                  i.     __.
    b.      __ is another technique.
    c.       For the leading strand, a special primer is needed only at the start of replication: why?
    If in the 3’à5’ direction, the end to be added to would have a triphosphate and mistakes could not be hydrolyzed away. Correction can only occur on the 3’ end

    Strand-directed mismatch repair

    once a replication fork is established, the DNA polymerase is continuously presented with a base-paired chain end on which to add new nucleotides
  18. a.       On the lagging side, every time the DNA polymerase completes a short DNA __, it must __
                                                                  i.      __ uses __ to synthesize __ ont eh lagging strand
    • okazaki fragment
    • start syntheizing a completely new fragment at a further site
    • DNA primase
    • ribonucleoside triphosphates
    • RNA primers
  19. a.       RNA is similar to DNA; and, a strand of RNA can __, generating a __ if the two nucleotide sequences are __
                                                                  i.      The RNA primer ends with a __ and is able to be elongated by __. Synthesis ends when the __
    • form base pairs with a strand of DNA
    • DNA/RNA hybrid double helix
    • complementary
    • 3’-OH group
    • DNA POL
    • DNA POL runs into the RNA primer at the 5’ end
  20. a.       To make the lagging strand continuous, a __acts quickly to __. __ then joins the fragments
    b.      The reason DNA isn’t used to make the primer is because __
                                                                  i.      With RNA as a primer, the ribonucleotides in the primer automatically__
    • special DNA repair system 
    • erase the old RNA primer and replace it with DNA
    • DNA ligase
    • any enzyme that starts chains anew cannot be efficient at self-corection and can make an inaccurate copy; and, mutations would be high
    •  mark these sequences as “suspect copy” to be removed and replaced
Card Set:
Molecular Text 5.1
2015-01-30 20:48:05
Test One
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