1. a.      Replication
                                                                  i.     __: short stretches of DNA having a specific sequence of nucleotides
    1.      Proteins __, __, and __the two strands, opening up a __
    a.      Replication in __ for both pro. And euk.
                                                                                                                                          i.      Bacterial: how many origins?n
                                                                                                                                        ii.      Eukaryote: how many origins?
    1.      What do they do?
    2.      Each end of replication bubble= __, a Y-shaped region where the parental strands of DNA are unwound
    •  origins of replication
    • recognize
    • attach
    • separate
    • replication bubble
    • both directions
    • one
    • several hundred or thousand
    • Form and fuse, speeding up the copying
    • replication fork
  2. Helicases
    untwist double helix at replciation forks, separating the two parental strands and making htem template strands
  3. Single-stranded binding proteins
    • bind to unpaired DNA strands, keeping them from re-pairing
    • - untwisiting causes tighter twisting and strain ahead of replication fork 
  4. Topoisomerase
    relieves strain by breaking, swiveling, and rejoining DNA strands
  5. What is the reason for RNA primase's existence?
    because enzymes that synthesize DNA can't initiate synthesis of a polynucleotide and only add to the end of an already existing chain that is base paired iwth the template strand
  6. RNA PRimase
    • 1.      sets a short stretch of RNA called the primase, which starts a complementary RNA chain from a single RNA nucleotide, adding RNA nucleotides one at a time.
    • a.      Now DNA nucleotides can begin being added
  7. DNA polymerases (general)
    catalyze synthesis of new DNA
  8. DNA pol III
    __ nucleotides per second and __ per sec in humans
    • 1.      adds a nucleotide to the RNA primer and continues adding DNA nucleotides to the growing end
    • a.      500 nucleotides per second and 50 per sec in humans
  9.                                                                                                                                       i.      Each nucleotide added to a growing DNA strands come from a __ which is a __
    • nucleoside triphosphate,
    • nucleoside with three phosphate groups
  10. Difference between ATP of energy metamolism and dATP
    • 1.      the sugar component, which is deoxyribose in the building block of DNA and ribose in ATP
  11. what is dATP
     the nucleoside triphosphate that supplies an adenine nucleotide to DNA
  12. Why are nucleoside triphosphates chemically reactive?
    due to cluster of negative charge
  13. DNA pol I
    1.      replaces RNA with DNA on primer
  14. DNA ligase
    1.      Only on lagging strand; bonds two Okazaki fragments together
  15. a.      Directionality and Antiparallelity
                                                                  i.      Because of their structure, DNA polymerases only add to the free __ end of a primer or growing DNA strand, never to the__ end
    1.     __direction
    • 3’
    •  5’
    •  5’à3’
  16.                                                               i.      Leading strand
    1.     __ elongation in 5’à3’ directioin
    2.      What does DNA pol III do?

    3.      How many primers required?
  17.  Continuous
    • DNA pol III remains in replication fork on the template strand and adds as fork progresses
    • one
  18.                                                               i.      Lagging strand
    1.      __works along the other template strand in the direction __ the __
    2.      __as segments called __
    a.      Each fragment must be __separately
    • DNA pol III
    • away from
    • replication fork
    • Discontinuous
    • Okazaki fragments (1000-2000 in e. coli and 100-200 in eukaryotes)
    • primed
  19. Process occurring in the lagging strand
    • a.      Primase forms primer
    • b.      DNA pol III adds DNA nucleotides to primer, forming first fragment
    • c.       After reaching next RNA primer, DNA pol III detaches
    • d.      Fragment two is primed and elongated, detaching upon contact of first fragment’s primer
    • e.       DNA pol I replaces the RNA with DNA, adding to the 3’ end
    • f.       DNA ligase bonds the two together to complete it
  20. a.      DNA Replication Complex
                                                                  i.   __as locomotoies moving along a railroad track is inaccurate
    1.      Various proteins that participate form a single large complex, a __
    a.    __ facilitate this
                                                                                                                                          i.      Example: by interacting with other proteins at the __, __acts as __, slowing progress of __and coordinating placement of __and rates of __
    2.      DNA replication complex doesn’t__ strand; strand__complex
    a.      Many complexes anchored to __
                                                                                                                                          i.      “__”
    •    DNA polymerases
    • “DNA replication machine”
    •   Protein-protein interactions
    • fork
    • primase
    • brake
    • fork
    • primers
    • replication
    •  move along
    •  moves through
    • nuclear matrix
    • reel in
  21.                                                               i.      During DNA replication, __proofread nucleotides as soon as added
    1.      Incorrectà __
                                                                ii.      If mistake evades proofreading, __occurs
    1.      Other enzymes remove and replace incorrectly paired nucleotides that have resulted from replication errors
    • DNA polymerases
    • removes
    • mismatch repair
  22. True or False:    Mistakes may arise after replication (such as through radiation or mutation)
  23.                                                               i.      Sometimes, a segment of the strand containing the damage is __ by a DNA-cutting enzyme—a __—and the resulting gap is filled in with the right nucleotides
    1.      Filling the gap: which enzymes?
    a.      One repair model is __
    • cut out (Excised)
    • nuclease
    • DNA polymerase and DNA ligase
    • nucleotide excision repair
  24.                                                               i.      One example of genetic damage through sunlight= __ cause DNA to buckle and interfere with DNA replication
    thymiine dimers
  25. a.      Replicating the Ends of DNA molecules
                                                                  i.      DNA polymerase cannot do what?
    1.      Even if starts with primer, the primer has to be removed and no DNA is added due to there not being a 3’ end
    a.      Repeated rounds of replication produce what?
    • complete the 5’ ends due to directionality
    •  shorter DNA molecules
  26.                                                               i.      Telomeres at ends in euk DNA
    1.      do not contain __, but instead have multiple repetitions of one short nucleotide sequence
    2.      acts as __ that protects the organism’s genes
    3.      in addition, specific proteins associated with __DNA prevent the staggered ends of the daughter from activating the cell’s systems for monitoring DNA damage
    4.      __function arises from postponing __ of genes located near the ends of DNA molecules
    5.      They become __ during every round of replication
    • genes 
    • multiple repetitions of one short nucleotide sequence
    • buffer zone
    • telomeric
    • protective
    • erosion
    • shorter and shorter
  27.                                                               i.      __catalyzes the lengthening of telomeres in eukaryotic germ cells to preserve genes, thus restoring their original length and compensating for shortening that occurs
    1.      Active in __cells
                                                                ii.      Normal shortening of telomeres may protect fro cancer by limiting number of somatic cell divisions
    • Telomerase
    • germ
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