1. Each nucleotide monomer consists of a __, __ and a __. The _ of one nucleotide is attached to the sugar of the next, resulting in a __ of alternating phosphates and sugars from which the bases project. The __ strand has directionality, fromt eh 5' end (with the __) to the 3' end (with the __). 5' and 3' refer to the numbers assigned to the carbons in the sugar ring.
    • nitrogenous base (A,C,T, or G)
    • phosphate group
    • deoxyribose
    • phosphate
    • "backbone"
    • polynucleotide
    • phosphate group
    • -OH group
  2. The DNA double helix is __, curving up to the right. The two strands are held together by __ between the nitrogenous bases, which are paired in the interior of the double helix.
    • right-handed
    • H bonds
  3. Strong __ link the units of each strand, while weaker __ hold one strand to the other. The strands are __, meaning that they are oriented in opposite directions.
    • covalent bonds
    • hydrogen bonds
    • antiparallel
  4. __ between the stacked pairs play a major role in holding the DNA molecule together.
    Van der Waals interactions
  5. The pairing of a purine + purine are __
    too wide
  6. The pairing of a pyrimidine and a pyrimidine are __
    too narrow
  7. The parent molecule has two __ strands of DNA. Each base is paired by __ with its specific partner, A with T, and G with C.
    • complementary
    • hydrogen bonds
  8. Model stating that the two parental strands reassociate after acting as templates for new strands, thus restoring the parental double helix.
    conservative model
  9. Model stating that the two strands of the parental molecule separate, and each functions as a template for synthesis of a new, complementary strand.
    semiconservative model
  10. Model stating that each strand of both daughter molecules contains a mixture of old and newly synthesized DNA
    dispersive model
  11. In the circular chromosome of E. coli and many other bacteria, only __ origin of replication is present.
  12. __ unwinds and separates the parental DNA strands.
  13. __ stabilize the unwound parental strands.
    Single-strand binding proteins
  14. __ breaks, swivels and rejoins the parental DNA ahead of the replication fork, relieving the strain caused by unwinding.
  15. __ synthesizes RNA primers, using the parental DNA as a template.
  16. __ catalyzes the addition of a nucleoside triphosphate to the 3' end of a growing DNA strand, with the release of two phosphates.
    DNA pol
  17. __ shaped like a cupped hand, is closely associated with a protein called the __ that encircles the newly synthesized double helix like a doughnut. The sliding clamp moves DNA pol III along teh DNA template strand.
    • DNA pol III
    • sliding clamp
  18. 1) __ joins RNA nucleotides in to a primer.
    2) __ adds DNA nucleotides to the primer, forming __ 1.
    3) After reaching teh next RNA primer to the right, __ detaches.
    4) After fragment 2 is primed __ adds DNA nucleotides until it reaches the fragment 1 primer and detaches.
    5) __ replaces the RNA with DNA, adding to the 3' end of fragment 2.
    6) __ forms a bond between the newest DNA and the DNA of fragment 1.
    7) The __ in this region is now complete.
    • Primase
    • DNA pol III
    • Okasazi fragment
    • DNA pol III x2
    • DNA pol I
    • DNA ligase
    • lagging strand
  19. 1) __ unwinds the parental double helix.
  20. 2) Molecules of __ stabilize the unwound template strands.
    single-strand binding protein
  21. 3) The leading strand is synthesized continuously in the 5'--> 3' direction by __.
    DNA pol III
  22. 4) __ begins synthesis of the RNA primer for the fifth __.
    • primase
    • okaszi fragment
  23. 5) __ is completing synthesis of the fourth fragment. WHen it reaches the RNA priner on the third fragment, it will dissociate, move to the __, and add DNA nucleotides to the 3' end of the fifth fragment primer.
    • DNA pol III
    • replication fork
  24. 3) __ removes the primer from the 5' end of the second fragment, replacing it with DNA nucleotides that it adds one by one to the 3' end of the third fragment. The replacement of the last RNA nucleotide with DNA leaves the sugar phosphate backbone with a free 3' end.
    DNA pol I
  25. 7) __ bonds the 3' end of the second fragment to the 5' end of the first fragment.
    DNA ligase
  26. unwinds parental double helix at the replcation forks
  27. binds to and stabilizes single-straded DNA until it can be used as a template
    single-strand binding protein
  28. relieves "overwinding" strain ahead of replication forks by breaking, swiveling and rejoining DNA strands
  29. synthesizes an RNA primer at 5' end of leading strand and of each Okazaki fragment of lagging strand
  30. Using parental DNA as a template, synthesizes new DNA strand by covalently adding nucleotides to the 3' end of a pre-existing DNA strand or RNA primer
    DNA pol III
  31. Removes RNA nucleotides of primer from 5' end and replaces them with DNA nucleotides
    DNA pol I
  32. Joins 3' end of DNA that replaces primer to rest of leading strand and joins Okazaki fragments of lagging strand
    DNA ligase
  33. Chromatin Packing in a Eukaryotic Chromosome
    Name the 6 levels.
    • DNA, the double helix
    • Histones
    • Nucleosomes, or "beads on a string" (10 nm fiber)
    • 30 nm fiber
    • Looped Domains (300 nm fiber)
    • Metaphse chromosome
  34. Proteins called __ are responsible for hte first level of DNA packing in chromatin. Athough each __ is small- containing about 100 amino acids- the total mass of __ in chromatin approximately equals the mass of DNA. More than a fifth of a __ amino acids are positively charged (lysine or arginine) and bind tightly to the negatively charged DNA.
    histones x3
  35. Four types of histones are most common in chromatin: __, __, __ and __. The histones are very similar among eukaryotes. The apparent conservation of __genes during evolution probably reflects the pivotal role of __ in organizing DNA within cells. The four main types of histones are critical to the next level of DNA packing. (A fifth type of histone, called __, is involved in a further stage of packing.)
    • H2A
    • H2B
    • H3
    • H4
    • histone x2
    • H1
  36. In EM, unfolded chromatin is __ in diameter. SUch chromatin resembles beads on a string. Each bead is a __, the basic unit of DNA packing; the string between beads is called __.
    • a nucleosone
    • linker DNA
  37. A __ consists of DNA wound twice around a protein core composed of two molecules each of the four main __ types. The amino end (N-terminus) of each histone (__) extends outward from the __.
    • nucleosome
    • histone
    • histone tail
    • nucleosome
  38. In the __, the __ leave the DNA only briefly during DNA replication. Generally, they do the same during gene expression, another process that requires access to DNA by the cell's molecular machinery.
    • cell cycle
    • histones
  39. The next level of packing (4) is due to interactions between the _- of one _- and teh __ and __ on either side. A fiftth histone, __, is involved at this level. These interactions cause the extended 10 nm fiber to coil or fold, forming a chromatin fiber roughly 30 nm in thickness, the __. Although the 30-nm fiber is quite prevalent in the interphase nucleus the packing arrangemnent of __ in this form of chromatin is still a matter of some debate.
    • histone tails
    • nucleosome
    • linker DNA
    • nucleosomes
    • H1
    • 30 nm fiber
    • nucleosomes
  40. The 30 nm fiber in turn forms loops called __ attached to a chromosome __ made of proteins, thus making upa __. The __ is rich in one type of __, and H1 molecules also appear to be present.
    • looped domains
    • scaffold
    • 300 nm fiber
    • scaffold
    • topoisomerase
  41. In a mitotic chromosome, the _ themselves ccoil and fold in a manner not yet fully understood, further compacting all the chromatin to produce the characteristic metaphase chromosome. The width of one chromatid is __. Particular genes always end up located at the same places in metaphase chromosomes, indicating that the packing steps are highly specific and precise.
    • looped domains
    • 700 nm
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AP Bio