genrepfinal.txt

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genrepfinal.txt
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2012-10-16 01:20:45
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  1. DNA is made into RNA by way of...
    Transcription
  2. RNA is made into DNA by way of...
    Reverse transcription
  3. RNA is made into proteins by way of...
    Translation
  4. DNA replication relies on the complememntary of DNA strands according to...
    The AT/GC Rule
  5. During the DNA replication process, the two complementary strands of DNA come apart and serve
  6. as... template strands (parental strands)
  7. During the DNA replication process, the two complementary strands of DNA come apart and serve
  8. as template strands (parental strands) for the synthesis of...
    Two new strands of DNA
  9. When do individual nucleotides have access to the template strands?
    After the double helix has separated
  10. For the DNA replication process to complete, a _________ is formed between the phosphate of one
  11. nucleotide and the sugar of the previous nucleotide.
    covalent bond
  12. For the DNA replication process to complete, a covalent bond is formed between the ________ of
  13. one nucleotide and the ________ of the previous nucleotide.
    • phosphate
    • sugar
  14. The two newly made strands the result from DNA replication are referred to as the...
    daughter strands
  15. The ________ are identical in both double-stranded molecules after replication.
    Base sequences
  16. the DNA synthesis of one newly made strand (the __________ strand) occurs in the direction
  17. toward the replication fork, whereas the synthesis of the other newly made strand (the _______
  18. strand) occurs in small segments away from the replication.
    • Leading
    • Lagging
  19. DNA replication produces two copies of DNA with the same _______ as the original DNA molecule.
    Sequence
  20. The Conservative model of DNA replication description...
    Both parental strands stay together after DNA replication
  21. The Semi-Conservative model of DNA replication description...
    The double-stranded DNA contains one parental and one daughter strand following replication
  22. The Dispersive model of DNA replication description...
    Parental and daughter DNA are interspersed in both strands following replication
  23. Who tested the hypothesis that DNA replication is Semi-Conservative and when?
    Matthew Meselson and Franklin Stahl in 1958
  24. Six steps of the Stahl and Meselon (e Coli) experiment?
    1) Add an excess of 14N- containing compounds to the bacterial cells so all of the newly made
  25. DNA will go from 15N to 14N
    • 2) Incubated the cells of various lengths of time
    • 3) Lyse the cells by the addition of lysozyme and detergent
    • 4) Load a sample of the lysate onto a CsCl gradient
    • 5) Centrifuge the gradients until the DNA molecules reach their equilibrium densities.
    • 6) DNA within the gradient can now be observed under a UV light.
  26. CsCl is...
    Cesium Chloride
  27. In the Stahl and Meselon (e Coli) experiment, E. Coli was grown in the presence of...
    15N
  28. In the Stahl and Meselon (e Coli) experiment, A haevy isotope of nitrogen that was used was...
    15N
  29. In the Stahl and Meselon (e Coli) experiment, a light isotope of nitrogen taht was used was...
    14N
  30. In the Stahl and Meselon (e Coli) experiment, the density of the DNA was analyzed by....
    centifugation using a CsCl gradient
  31. In the Stahl and Meselon (e Coli) experiment, the top of the testtube was ______ dense than the
  32. bottom
    less
  33. In the Stahl and Meselon (e Coli) experiment, the bottom of the testtube was ______ dense than
  34. the top
    more
  35. In the Stahl and Meselon (e Coli) experiment, the lower Cs+ concentration was located at the
  36. _______ of the test tube.
    top
  37. In the Stahl and Meselon (e Coli) experiment, the higher Cs+ concentration was located at rhe
  38. ________ of the test tube.
    bottom
  39. the _________ lies between the light and heavy sections of the testtube.
    DNA intermediate
  40. In the Stahl and Meselon (e Coli) experiment, __N shift cells to __N
    15N to 14N
  41. two rounds of DNA replication = ___ generations.
    1.9
  42. In the Stahl and Meselon (e Coli) experiment, the result that would be consistent with the
  43. semiconservative model of DNA replication after two generations is...
    mixture of light DNA and half-heavy DNA
  44. In the Stahl and Meselon (e Coli) experiment, the result that would be consistent with the The
  45. dispersive model after two generations is..
    the heavy nitrogen would be evenly dispersed among four strands, each strand containing 1/4
  46. heavy nitrogen and 3/4 light nitrogen
  47. In the Stahl and Meselon (e Coli) experiment, the result that would be consistent with the The
  48. conservative model after two generations is..
    two separate DNA types: a light type and a heavy type.
  49. In the Stahl and Meselon (e Coli) experiment, the conservative model was disproved because...
    all of the DNA had sedimented as a single band
  50. in bacterial replication, the origin of replication is...
    the site on the bacterial chromosome where DNA synthesis begins
  51. Each bacterial chromosome has ___ origin of replication(s)
    1
  52. in bacterial replication, synthesis of DNA proceeds ________ around the bacterial chromosome.
    biodirectionally
  53. Biodirectional means....
    "proceeds in both directions"
  54. In bacterial replication, the synthesis of DNA proceeds biodirectionally and eventually
  55. meets...
    at the opposite side of the bacterial chromosome
  56. in bacterial replication, replication ends at...
    the opposite side of the bacterial chromosome
  57. in bacterial replication, two replication forks move in opposite directions....
    outward from the origin
  58. in bacterial replication, two replication forks move _________ outward from the origin
    in opposite directions
  59. in bacterial replication, A replication fork is the site where....
    the parental DNA strands have separated and new daughter strands are being made
  60. replication forks meet each other on the opposite side of the bacterial chromosome to...
    complete the replication process.
  61. _________ meet each other on the opposite side of the bacterial chromosome to complete the
  62. replication process.
    replication forks
  63. Replication is Semi-____________.
    Discontinuous
  64. Replication is initiated by the binding of...
    DnaA protein to the origin of replication
  65. the origin of replication in E. coli is called...
    oriC
  66. oriC stands for...
    Origin of Chromosomal replication
  67. Three types of DNA sequences found within oriC are
    • an AT-rich region
    • DnaA box sequences
    • GATC methylation sites
  68. DNA replication is initiated by the binding of DnaA proteins to sequences within the origin
  69. known as....
    DnaA box sequences.
  70. ________serve as recognition sites for the binding of the DnaA proteins
    DnaA box sequences
  71. When DnaA proteins are in their ATP-bound form, they bind to...
    the five DnaA boxes in oriC to initiate DNA replication
  72. the seperation of the AT-rich region is caused by...
    THE DNA bending around the complex of DnaA proteins by the aid of DNA-binding proteins (HU and
  73. IHF)
  74. The DNA strands are more easily seperated at an AT-rich region because...
    Only two hydrogen bonds occur between Adenine and Thymine.
  75. The DNA strands are more easily seperated at...
    an AT-rich region
  76. Following separation of the AT-rich region, the _____ protein, with the help of the ______
  77. protein, recruit __________ proteins to this site.
    • DnaA
    • DnaC
    • DNA helicase
  78. DNA helicase is also known as...
    DnaB protein.
  79. What happens when a DNA helicase encounters a double stranded region?
    it breaks the hydrogen bonds between the two strands, making two single strands.
  80. What begins strand separation within the oriC region and continue to separate the
    • DNA strands beyond the origin?
    • DNA Helicases
  81. How many DNA helicases begin strand separation within the oriC region and continue to separate
  82. the DNA strands beyond the origin?
    Two
  83. DNA helicases use the energy from ATP hydrolysis to...
    catalyze the separation of the double-stranded parental DNA
  84. DNA helicases use the energy from ___________ to catalyze the separation of the double-stranded
  85. parental DNA
    ATP hydrolysis
  86. In E. coli, DNA helicases bind to __________ DNA.
    Single-stranded
  87. In E.coli DNA helicases bind to single-stranded DNA and travel along the DNA in a __________
  88. direction
    5' to 3'
  89. In E.coli DNA helicases bind to single-stranded DNA and travel along the DNA in a 5' to 3'
  90. direction in order to ....
    keep the replication fork moving
  91. The action of DNA helicases promotes the movement of two replication forks outward from....
    oriC in opposite directions.
  92. The action of DNA helicases promotes the movement of ___________________ outward from oriC in
  93. opposite directions.
    Two replication forks
  94. The action of DNA helicases promoting the movement of two replication forks outward from oriC
  95. in opposite directions inititates...
    the replication of the bacterial chromosome in both directions (bidirectional replication)
  96. Bidirectional replication in bacterial chromosome is when...
    the replication of the bacterial chromosome is initiated in both directions
  97. List the three steps that occur at oriC to initiate the DNA replication process.
    1) DnaA proteins bind to DnaA boxes and to each other. (causes the AT-rich region to wrap
  98. around the DnaA proteins and separates the AT-rich region)
    • 2) DNA helicase (DnaB protein) binds to the origin while DnaC protein assists.
    • 3) DNA helicase separates the DNA in both directions, creating 2 replication forks
  99. The function of DNA helicase is to....
    break the hydrogen bonds between base pairs and unwind the strands.
  100. The action of the DNA helicases breaking the H bonds between base pairs and unwinding the
  101. strands generates _____________ ahead of each replication fork
    positive supercoiling
  102. The action of the DNA helicases breaking the H bonds between base pairs and unwinding the
  103. strands generates positive supercoiling ahead of each...
    replication fork
  104. DnaA protein's function in E. coli DNA replication is..
    Binds to DnaA boxes within the origin to initiate DNA replication
  105. DnaC protein's function in E. coli DNA replication is..
    Aids DnaA in the recruitment of DNA helicase to the origin
  106. DNA helicase (DnaB) protein's function in E. coli DNA replication is..
    Seperates double-stranded DNA
  107. Topoisomerase's function in E. coli DNA replication is..
    Removes positive supercoiling ahead of the replication fork
  108. Single-strand binding protein's function in E. coli DNA replication is..
    Binds to single-stranded DNA and prevents it from re-forming a double-stranded structure.
  109. Primase's function in E. coli DNA replication is..
    synthesizes short RNA primers
  110. DNA Polymerase III's function in E. coli DNA replication is..
    Synthesizes DNA in the leading and lagging strands
  111. DNA Polymerase I's function in E. coli DNA replication is..
    Removes RNA primers, fills in gaps with DNA
  112. DNA ligase's function in E. coli DNA replication is..
    Covalently attaches adjacent Okazaki fragments
  113. Tus' function in E. coli DNA replication is..
    Binds to ter sequences and prevents the advancemnet of the replication fork
  114. Topoisomerase (Type II) is also called...
    DNA gyrase
  115. the bases within the parental strands are kept in an exposed condition that enables them to
  116. hydrogen bond with individual nucleotides because of the function of ...
    single-strand binding proteins
  117. _______ synthesizes short strands of RNA, typically 10 to 12 nucleotides in
    • length.
    • Primase
  118. Primase synthesizes short strands of RNA, typically _____________ in length
    10 to 12 nucleotides
  119. In the _________ strand, a single primer is made at the origin of replication.
    leading
  120. In the _________ strand, multiple primers are made.
    lagging
  121. What enzyme catalyzes the formation of covalent bonds between adjacent nucleotides and thereby
  122. makes the new daughter strands?
    DNA polymerase
  123. In E. coli, _____ distinct proteins function as DNA polymerases.
    five
  124. DNA polymerases ___ and ____ are involved in normal DNA replication
    I and III
  125. DNA polymerases ___, ___, and ____ play a role in DNA repair and the replication of damaged
  126. DNA.
    II, IV and V
  127. DNA polymerase ____ is responsible for most of the DNA replication.
    III
  128. Primers are... (RNA or DNA)?
    RNA
  129. In the semi-discontinous replication, the sucrose gradient at the ______ is smaller.
    Top
  130. In the semi-discontinous replication, the sucrose gradient at the ______ is larger.
    Bottom
  131. In the semi-discontinous replication, _________ fragments are seen in sucrose density
  132. gradients.
    3H labeled
  133. In the semi-discontinous replication, 3H labeled fragments are seen in __________ gradients.
    Sucrose density
  134. You identify proteins and enzymes involved in Replication by combining _________ and ________.
    Genetics and Biochemistry
  135. The genetic approach to identifying proteins and enzymes involved in replication is...
    Obtain mutants that are defective in Replication
  136. The three step method to identifying proteins and enzymes involved in replication is..
    • 1) Mutagenize cells
    • 2) Plate the cells on agar and grow at 30oC
    • 3) Replica plated and grown 37oC
  137. What are the five steps to identifying which ts lethal mutants have defects in their
  138. replication?
    • 1) Pick ts colonies from 30oC plate and grow them in liquid medium at 30oC
    • 2) Shift them to 37oC
    • 3) Add Rromodeoxyuridine (BrdU) and continue growth for a short time at 37oC
    • 4) Remove the BrdU and irradiate the cells with UV light
    • 5) Return the cells to 30oC
  139. What does it mean if ts cells are killed by UV light?
    BrdU is incorporated into the DNA, thus replicating it and ultimately killing theirselves
  140. What does it mean it ts cells are NOT killed by UV light?
    Did not incorporate BrdU because they have a defect in Replication
  141. In the ts UV light experiemsnt, why did the ts cells that are not killed by UV light did not
  142. incorporate BrdU?
    Because they have a defect in Replication
  143. The in vitro study of DNA replication was pioneered by ....
    Arthur Kornberg
  144. What did Kornberg mis and incubate to allow a synthesis of new DNA strands?
    • Extract of proteins from E. coli
    • Template DNA
    • Radiolabeled nucleotides
  145. ts mutant stands for...
    Temperature sensitive mutant
  146. E.coli Proteins + DNA at 37oC= Replication (Wildtype, ts mutant or both)
    Wildtype
  147. E.coli Proteins + DNA at 30oC= Replication (Wildtype, ts mutant or both)
    ts mutant
  148. E.coli Proteins + DNA at 37oC= NO Replication (Wildtype, ts mutant or both)
    ts mutant
  149. E.coli Proteins + DNA at 37oC= Replication (Wildtype, ts mutant or both)
    Both
  150. How are ts mutant proteins involved in a succesful DNA replication purified?
    Mixed with wildtype proteins
  151. The AT-rich region is composed of _________ tandem repeats
    three
  152. The AT-rich region is composed of three tandem repeats that are ____ bp long
    13
  153. DnaB protein (helicase) binds to the...
    origin
  154. DNA replication is initiated by...
    the binding of DnaA proteins to the DnaA box sequences
  155. DNA replication requires single-strand binding proteins that bind to the strands of parental
  156. DNA and prevent them from ...
    re-forming a double helix.
  157. DNA replication requires ________ that bind to the strands of parental DNA and prevent them
  158. from re-forming a double helix.
    single-strand binding proteins
  159. In a plectonemic coil, the two strands....
    wrap around each other
  160. In a paranemic joint, the two strands....
    align side by side
  161. In a __________, the two strands wrap around each other
    plectonemic coil
  162. In a __________, the two strands align side by side
    paranemic joint
  163. Single-strand binding proteins bind to the separated DNA strands to...
    keep them apart
  164. Single-strand binding proteins bind to the ________ to keep them
    separated DNA strands
  165. ______________ bind to the separated DNA strands to keep them apart
    Single-strand binding proteins
  166. Elongation occurs when...
    DNA polymerase cannot initiate new strands
  167. What does the bulk of the copying DNA in replication?
    DNA polymerase III
  168. The direction of the synthesis on the leading strand is...
    5' to 3' (right to left)
  169. The direction of the synthesis on the lagging strand is...
    5' to 3' (left to right)
  170. In proofreading, When a base pair mismatch is found, the end of the newly made strand is
  171. shifted into the...
    3ʹ exonuclease site.
  172. In proofreading, Whenthe end of the newly made strand is shifted into the 3ʹ exonuclease site
  173. what happens to the DNA?
    The DNA is digested in the 3ʹ to 5ʹ direction to release the incorrect nucleotide.
  174. The proofreading fucntion is...
    identifying a mismatched nucleotide and removing it from the daughter strand.
  175. Nicks are...
    single strand breaks in double stranded DNA
  176. Single strand breaks in double stranded DNA are called...
    Nicks
  177. DNA polymerases can only synthesize DNA only in the ________ direction
    5’ to 3’
  178. DNA polymerases cannot initiate ....
    DNA synthesis
  179. The two features that pose a problem at the 3' end of linear chromosomes are...
    The fact that DNA polymerases can only synthesize DNA only in the 5’ to 3’ direction and cannot
  180. initiate DNA synthesis.
  181. If the problem at the 3' end of a linear chromosome is not solved, what happens?
    The linear chromosome becomes progressively shorter with each round of DNA replication
  182. How does the cell solve the problem at the 3' end of a linear chromosome?
    adding DNA sequences to the ends of chromosome
  183. DNA sequences to the ends of choromsomes are called....
    telomeres
  184. The addition of telomeres to the end of chromosomes are catalyzed by the enzyme....
    telomerase
  185. Telomerase contains what two things?
    Protein and RNA
  186. The RNA in telomerase functions as...
    the template
  187. What allows the telomerase to bind to the 3' overhang on the linear chromosome?
    It's RNA template that is complementary to the DNA sequence found in the telomeric repeat
  188. What are the three steps to the binding-polymerization-translocation cycle?
    • 1) Binding of the telomere to the 3' overhang
    • 2) Polymerization of a 6-nucleotide repeat
    • 3) Translocation is which the complementary strand is made by primase, DNA polymerase and
  189. ligase, RNA Primer results.
  190. What are the 6 steps of the synthesis and replacement of RNA primers during DNA replication?
    • 1) intitiation of RNA primer synthesis by DNA primase
    • 2) 5' to 3' extension of RNA primer and dissociation of DNA primase
    • 3) DNA polymerase II make a 5' to 3' synthesis of DNA that is initiated at the free 3'-OH of
  191. the RNA primer
    4) Simultaneous removal of RNA primer by 5' to 3' exonuclease activity of DNA poymerase I and
  192. 5' to 3' synthesis by polymerase activity of DNA polymerase I
    5) covalent closure by DNA ligase
  193. What are the ten steps of the viral lifecyle?
    • 1) gp120 on virus surface binds with the CD4 receptor
    • 2) Virus is taken into the cell
    • 3) The viral genome comes out of the viral core into the cytoplasm
    • 4) The Viral RNA goes through reverse transcriptase to produce Viral DNA
    • 5) The Viral DNA enters the Nuclus and binds to the Cellular DNA by integrase
    • 6) More Viral RNA is replicated in the nucleus
    • 7) The Viral RNA is relaeased into the cytoplasm
    • 8) A Viral Core is formed in the cytoplasm
    • 9) The Viral Core goes through Exocytosis so a new virus membrane is created
    • 10) The new virus is released into the extracellular fluid to repeat the cycle.

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