genrepFINAL.txt

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genrepFINAL.txt
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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 as...
    template strands (parental strands)
  6. During the DNA replication process, the two complementary strands of DNA come apart and serve as template strands (parental strands) for the synthesis of...
    Two new strands of DNA
  7. When do individual nucleotides have access to the template strands?
    After the double helix has separated
  8. For the DNA replication process to complete, a _________ is formed between the phosphate of one nucleotide and the sugar of the previous nucleotide.
    covalent bond
  9. For the DNA replication process to complete, a covalent bond is formed between the ________ of one nucleotide and the ________ of the previous nucleotide.
    • phosphate
    • sugar
  10. The two newly made strands the result from DNA replication are referred to as the...
    daughter strands
  11. The ________ are identical in both double-stranded molecules after replication.
    Base sequences
  12. the DNA synthesis of one newly made strand (the __________ strand) occurs in the direction toward the replication fork, whereas the synthesis of the other newly made strand (the _______ strand) occurs in small segments away from the replication.
    • Leading
    • Lagging
  13. DNA replication produces two copies of DNA with the same _______ as the original DNA molecule.
    Sequence
  14. The Conservative model of DNA replication description...
    Both parental strands stay together after DNA replication
  15. The Semi-Conservative model of DNA replication description...
    The double-stranded DNA contains one parental and one daughter strand following replication
  16. The Dispersive model of DNA replication description...
    Parental and daughter DNA are interspersed in both strands following replication
  17. Who tested the hypothesis that DNA replication is Semi-Conservative and when?
    Matthew Meselson and Franklin Stahl in 1958
  18. 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 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.
  19. CsCl is...
    Cesium Chloride
  20. In the Stahl and Meselon (e Coli) experiment, E. Coli was grown in the presence of...
    15N
  21. In the Stahl and Meselon (e Coli) experiment, A haevy isotope of nitrogen that was used was...
    15N
  22. In the Stahl and Meselon (e Coli) experiment, a light isotope of nitrogen taht was used was...
    14N
  23. In the Stahl and Meselon (e Coli) experiment, the density of the DNA was analyzed by....
    centifugation using a CsCl gradient
  24. In the Stahl and Meselon (e Coli) experiment, the top of the testtube was ______ dense than the bottom
    less
  25. In the Stahl and Meselon (e Coli) experiment, the bottom of the testtube was ______ dense than the top
    more
  26. In the Stahl and Meselon (e Coli) experiment, the lower Cs+ concentration was located at the _______ of the test tube.
    top
  27. In the Stahl and Meselon (e Coli) experiment, the higher Cs+ concentration was located at rhe ________ of the test tube.
    bottom
  28. the _________ lies between the light and heavy sections of the testtube.
    DNA intermediate
  29. In the Stahl and Meselon (e Coli) experiment, __N shift cells to __N
    15N to 14N
  30. two rounds of DNA replication = ___ generations.
    1.9
  31. In the Stahl and Meselon (e Coli) experiment, the result that would be consistent with the semiconservative model of DNA replication after two generations is...
    mixture of light DNA and half-heavy DNA
  32. In the Stahl and Meselon (e Coli) experiment, the result that would be consistent with the The dispersive model after two generations is..
    the heavy nitrogen would be evenly dispersed among four strands, each strand containing 1/4 heavy nitrogen and 3/4 light nitrogen
  33. In the Stahl and Meselon (e Coli) experiment, the result that would be consistent with the The conservative model after two generations is..
    two separate DNA types: a light type and a heavy type.
  34. In the Stahl and Meselon (e Coli) experiment, the conservative model was disproved because...
    all of the DNA had sedimented as a single band
  35. in bacterial replication, the origin of replication is...
    the site on the bacterial chromosome where DNA synthesis begins
  36. Each bacterial chromosome has ___ origin of replication(s)
    1
  37. in bacterial replication, synthesis of DNA proceeds ________ around the bacterial chromosome.
    biodirectionally
  38. Biodirectional means....
    "proceeds in both directions"
  39. In bacterial replication, the synthesis of DNA proceeds biodirectionally and eventually meets...
    at the opposite side of the bacterial chromosome
  40. in bacterial replication, replication ends at...
    the opposite side of the bacterial chromosome
  41. in bacterial replication, two replication forks move in opposite directions....
    outward from the origin
  42. in bacterial replication, two replication forks move _________ outward from the origin
    in opposite directions
  43. in bacterial replication, A replication fork is the site where....
    the parental DNA strands have separated and new daughter strands are being made
  44. replication forks meet each other on the opposite side of the bacterial chromosome to...
    complete the replication process.
  45. _________ meet each other on the opposite side of the bacterial chromosome to complete the replication process.
    replication forks
  46. Replication is Semi-____________.
    Discontinuous
  47. Replication is initiated by the binding of...
    DnaA protein to the origin of replication
  48. the origin of replication in E. coli is called...
    oriC
  49. oriC stands for...
    Origin of Chromosomal replication
  50. Three types of DNA sequences found within oriC are
    • an AT-rich region
    • DnaA box sequences
    • GATC methylation sites
  51. DNA replication is initiated by the binding of DnaA proteins to sequences within the origin known as....
    DnaA box sequences.
  52. ________serve as recognition sites for the binding of the DnaA proteins
    DnaA box sequences
  53. When DnaA proteins are in their ATP-bound form, they bind to...
    the five DnaA boxes in oriC to initiate DNA replication
  54. 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 IHF)
  55. The DNA strands are more easily seperated at an AT-rich region because...
    Only two hydrogen bonds occur between Adenine and Thymine.
  56. The DNA strands are more easily seperated at...
    an AT-rich region
  57. Following separation of the AT-rich region, the _____ protein, with the help of the ______ protein, recruit __________ proteins to this site.
    • DnaA
    • DnaC
    • DNA helicase
  58. DNA helicase is also known as...
    DnaB protein.
  59. What happens when a DNA helicase encounters a double stranded region?
    it breaks the hydrogen bonds between the two strands, making two single strands.
  60. What begins strand separation within the oriC region and continue to separate the
    • DNA strands beyond the origin?
    • DNA Helicases
  61. How many DNA helicases begin strand separation within the oriC region and continue to separate the DNA strands beyond the origin?
    Two
  62. DNA helicases use the energy from ATP hydrolysis to...
    catalyze the separation of the double-stranded parental DNA
  63. DNA helicases use the energy from ___________ to catalyze the separation of the double-stranded parental DNA
    ATP hydrolysis
  64. In E. coli, DNA helicases bind to __________ DNA.
    Single-stranded
  65. In E.coli DNA helicases bind to single-stranded DNA and travel along the DNA in a __________ direction
    5' to 3'
  66. In E.coli DNA helicases bind to single-stranded DNA and travel along the DNA in a 5' to 3' direction in order to ....
    keep the replication fork moving
  67. The action of DNA helicases promotes the movement of two replication forks outward from....
    oriC in opposite directions.
  68. The action of DNA helicases promotes the movement of ___________________ outward from oriC in opposite directions.
    Two replication forks
  69. The action of DNA helicases promoting the movement of two replication forks outward from oriC in opposite directions inititates...
    the replication of the bacterial chromosome in both directions (bidirectional replication)
  70. Bidirectional replication in bacterial chromosome is when...
    the replication of the bacterial chromosome is initiated in both directions
  71. 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 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
  72. The function of DNA helicase is to....
    break the hydrogen bonds between base pairs and unwind the strands.
  73. The action of the DNA helicases breaking the H bonds between base pairs and unwinding the strands generates _____________ ahead of each replication fork
    positive supercoiling
  74. The action of the DNA helicases breaking the H bonds between base pairs and unwinding the strands generates positive supercoiling ahead of each...
    replication fork
  75. DnaA protein's function in E. coli DNA replication is..
    Binds to DnaA boxes within the origin to initiate DNA replication
  76. DnaC protein's function in E. coli DNA replication is..
    Aids DnaA in the recruitment of DNA helicase to the origin
  77. DNA helicase (DnaB) protein's function in E. coli DNA replication is..
    Seperates double-stranded DNA
  78. Topoisomerase's function in E. coli DNA replication is..
    Removes positive supercoiling ahead of the replication fork
  79. 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.
  80. Primase's function in E. coli DNA replication is..
    synthesizes short RNA primers
  81. DNA Polymerase III's function in E. coli DNA replication is..
    Synthesizes DNA in the leading and lagging strands
  82. DNA Polymerase I's function in E. coli DNA replication is..
    Removes RNA primers, fills in gaps with DNA
  83. DNA ligase's function in E. coli DNA replication is..
    Covalently attaches adjacent Okazaki fragments
  84. Tus' function in E. coli DNA replication is..
    Binds to ter sequences and prevents the advancemnet of the replication fork
  85. Topoisomerase (Type II) is also called...
    DNA gyrase
  86. the bases within the parental strands are kept in an exposed condition that enables them to hydrogen bond with individual nucleotides because of the function of ...
    single-strand binding proteins
  87. _______ synthesizes short strands of RNA, typically 10 to 12 nucleotides in
    • length.
    • Primase
  88. Primase synthesizes short strands of RNA, typically _____________ in length
    10 to 12 nucleotides
  89. In the _________ strand, a single primer is made at the origin of replication.
    leading
  90. In the _________ strand, multiple primers are made.
    lagging
  91. What enzyme catalyzes the formation of covalent bonds between adjacent nucleotides and thereby makes the new daughter strands?
    DNA polymerase
  92. In E. coli, _____ distinct proteins function as DNA polymerases.
    five
  93. DNA polymerases ___ and ____ are involved in normal DNA replication
    I and III
  94. DNA polymerases ___, ___, and ____ play a role in DNA repair and the replication of damaged DNA.
    II, IV and V
  95. DNA polymerase ____ is responsible for most of the DNA replication.
    III
  96. Primers are... (RNA or DNA)?
    RNA
  97. In the semi-discontinous replication, the sucrose gradient at the ______ is smaller.
    Top
  98. In the semi-discontinous replication, the sucrose gradient at the ______ is larger.
    Bottom
  99. In the semi-discontinous replication, _________ fragments are seen in sucrose density gradients.
    3H labeled
  100. In the semi-discontinous replication, 3H labeled fragments are seen in __________ gradients.
    Sucrose density
  101. You identify proteins and enzymes involved in Replication by combining _________ and ________.
    Genetics and Biochemistry
  102. The genetic approach to identifying proteins and enzymes involved in replication is...
    Obtain mutants that are defective in Replication
  103. 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
  104. What are the five steps to identifying which ts lethal mutants have defects in their 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
  105. 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
  106. What does it mean it ts cells are NOT killed by UV light?
    Did not incorporate BrdU because they have a defect in Replication
  107. In the ts UV light experiemsnt, why did the ts cells that are not killed by UV light did not incorporate BrdU?
    Because they have a defect in Replication
  108. The in vitro study of DNA replication was pioneered by ....
    Arthur Kornberg
  109. What did Kornberg mis and incubate to allow a synthesis of new DNA strands?
    • Extract of proteins from E. coli
    • Template DNA
    • Radiolabeled nucleotides
  110. ts mutant stands for...
    Temperature sensitive mutant
  111. E.coli Proteins + DNA at 37oC= Replication (Wildtype, ts mutant or both)
    Wildtype
  112. E.coli Proteins + DNA at 30oC= Replication (Wildtype, ts mutant or both)
    ts mutant
  113. E.coli Proteins + DNA at 37oC= NO Replication (Wildtype, ts mutant or both)
    ts mutant
  114. E.coli Proteins + DNA at 37oC= Replication (Wildtype, ts mutant or both)
    Both
  115. How are ts mutant proteins involved in a succesful DNA replication purified?
    Mixed with wildtype proteins
  116. The AT-rich region is composed of _________ tandem repeats
    three
  117. The AT-rich region is composed of three tandem repeats that are ____ bp long
    13
  118. DnaB protein (helicase) binds to the...
    origin
  119. DNA replication is initiated by...
    the binding of DnaA proteins to the DnaA box sequences
  120. DNA replication requires single-strand binding proteins that bind to the strands of parental DNA and prevent them from ...
    re-forming a double helix.
  121. DNA replication requires ________ that bind to the strands of parental DNA and prevent them from re-forming a double helix.
    single-strand binding proteins
  122. In a plectonemic coil, the two strands....
    wrap around each other
  123. In a paranemic joint, the two strands....
    align side by side
  124. In a __________, the two strands wrap around each other
    plectonemic coil
  125. In a __________, the two strands align side by side
    paranemic joint
  126. Single-strand binding proteins bind to the separated DNA strands to...
    keep them apart
  127. Single-strand binding proteins bind to the ________ to keep them
    separated DNA strands
  128. ______________ bind to the separated DNA strands to keep them apart
    Single-strand binding proteins
  129. Elongation occurs when...
    DNA polymerase cannot initiate new strands
  130. What does the bulk of the copying DNA in replication?
    DNA polymerase III
  131. The direction of the synthesis on the leading strand is...
    5' to 3' (right to left)
  132. The direction of the synthesis on the lagging strand is...
    5' to 3' (left to right)
  133. In proofreading, When a base pair mismatch is found, the end of the newly made strand is shifted into the...
    3ʹ exonuclease site.
  134. In proofreading, Whenthe end of the newly made strand is shifted into the 3ʹ exonuclease site what happens to the DNA?
    The DNA is digested in the 3ʹ to 5ʹ direction to release the incorrect nucleotide.
  135. The proofreading fucntion is...
    identifying a mismatched nucleotide and removing it from the daughter strand.
  136. Nicks are...
    single strand breaks in double stranded DNA
  137. Single strand breaks in double stranded DNA are called...
    Nicks
  138. DNA polymerases can only synthesize DNA only in the ________ direction
    5’ to 3’
  139. DNA polymerases cannot initiate ....
    DNA synthesis
  140. 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 initiate DNA synthesis.
  141. 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
  142. How does the cell solve the problem at the 3' end of a linear chromosome?
    adding DNA sequences to the ends of chromosome
  143. DNA sequences to the ends of choromsomes are called....
    telomeres
  144. The addition of telomeres to the end of chromosomes are catalyzed by the enzyme....
    telomerase
  145. Telomerase contains what two things?
    Protein and RNA
  146. The RNA in telomerase functions as...
    the template
  147. 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
  148. 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 ligase, RNA Primer results.
  149. 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 the RNA primer
    • 4) Simultaneous removal of RNA primer by 5' to 3' exonuclease activity of DNA poymerase I and 5' to 3' synthesis by polymerase activity of DNA polymerase I
    • 5) covalent closure by DNA ligase
  150. 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.
  151. DNA polymerase would slide from...
    right to left 5' to 3'
  152. In replication, which Okazaki fragment is made first? (middle left or right?)
    the right
  153. in replication, why is the Okazaki fragment on the right made first?
    It is farthest away fromthe replication fork
  154. Which RNA primer would be the first one to be removed byDNA polymerase I, the primer on the left or the primer on the right?
    The RNA primer in the right Okazaki fragment would be removed first.
  155. Why would The RNA primer in the right Okazaki fragment would be removed first by the DNA polymerase I ?
    Because the DNA polymerase would begin by elongating the DNA strand of the middle Okazaki fragment and removing the right RNAprimer with its 5' to 3' exonuclease activity.
  156. For the right primer to be removed by DNA polymerase I and for the gap to be filled in, is it necessary for the Okazaki fragment in the middle to have already been synthesized?
    Yes, If the middle fragment was not present, DNA polymerase could not fill in this DNA (because it needs a primer).
  157. After DNA polymerase I removes the middle RNA primer and fills in the gap with DNA, where does DNA ligase function?
    You need DNA ligase only at the right arrow. DNA polymerase Ibegins at the end of the left Okazaki fragment and synthesizes DNA to fill in the region as it removes the middle RNA primer.
  158. What is DNA polymerase I doing at the left arrow?
    DNA polymerase I is simply extending the length of the left Okazaki fragment
  159. Why is no DNA ligase needed at the left arrow?
    DNA polymerase I is simply extending the length of the left Okazaki fragment.
  160. What is needed to connect the monophosphate with the 3' end of the region where the middle RNA primer has been removed?
    DNA ligase
  161. Why DNA ligase need another source of energyto connect two nucleotides, but DNA polymerase needs nothing more than the incoming nucleotide and the existing DNA strand?
    DNA ligase needs energy to connect (covalently bond) the nucleotide with the Okazaki fragment, whereas DNA polymerase is just enolngating.
  162. The leading strand is primed ______, at the origin
    once
  163. The leading strand is primed once, at ......
    the origin
  164. The leading strand is primed once, at the origin and then _______ synthesizes DNA continuously in the direction of thereplication fork.
    DNA polymerase III
  165. The leading strand is primed once, at the origin, and then DNApolymerase III synthesizes DNA continuously in the direction of .....
    the replication fork.
  166. Okazaki fragments are..
    short pieces of DNA
  167. In the lagging strand, many _______ are made.
    short pieces of DNA(Okazaki fragments)
  168. In the _______ strand, many short pieces of DNA(Okazaki fragments) are made.
    lagging
  169. In the lagging strand, many short pieces of DNA(Okazaki fragments) are made. This requires many....
    RNA primers
  170. _______ are removed by DNA polymerase I, which then fills in the gaps with DNA
    RNA primers
  171. RNA primers are removed by ________, which then fills in the gaps with DNA
    DNA polymerase I
  172. RNA primers are removed by DNA Polymerase I, which then .....
    fills in the gaps with DNA
  173. RNA primers are removed by DNA Polymerase I, which then fills in the gaps with...
    DNA
  174. After the RNA primers are removed and the gaps are filled, ________ then covalently connects the Okazaki fragments
    DNA Ligase
  175. After the RNA primers are removed and the gaps are filled, DNA Ligase then ______ connects the Okazaki fragments
    covalently
  176. After the RNA primers are removed and the gaps are filled, DNA Ligase then covalently connects the....
    Okazaki fragments
  177. Having the enzymes within a complex such as a primosome or replisome provides...
    coordination among the different steps in the replication process
  178. Having the enzymes within a complex such as a primosome or replisome provides coordination among the different steps in thereplication process and thereby allows it to...
    proceed faster and more efficiently.
  179. A processive enzyme is one that....
    remains clamped to one of its substrates. (does not dissociate)
  180. In the case of DNA polymerase, in terms of it being a processive enzyme, it remains _______ to the template strand as it makes a new daughter strand
    clamped
  181. In the case of DNA polymerase, in terms of it being a processive enzyme, it remains clamped to the ______ strand as it makes a new daughter strand
    template
  182. In the case of DNA polymerase, in terms of it being a processive enzyme, it remains clamped to the template strand as it makes a new _____ strand
    daughter
  183. The function of the processive enzyme is important in that it...
    ensures a fast rate of DNA synthesis.
  184. What enzymatic features of DNA polymerase prevent it from replicating one of the DNA strands at the ends of linear chromosomes?
    the inability to synthesize DNA in the 3' to 5' directionand the need for a primer to prevent replication at the 3' end of the DNAstrands
  185. Compared with DNA polymerase, how is telomerase different in its ability to synthesize a DNA strand?
    Telomerase is different than DNA polymerase in that it usesa short RNA sequence, which is part of its structure, as a template for DNA synthesis.
  186. What does telomerase use as its template for the synthesis of a DNA strand?
    RNA sequencing
  187. How does the use of this template result in a telomere sequence that is tandemly repetitive?
    Because it uses this sequence many times in row, it produces a tandemly repeated sequence in the telomere at the 3' ends of linear chromosomes.

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