1. Nucleotides are added to the 3\' end of a growing DNA chain via nucleophilic
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Question
1. Nucleotides are added to the 3' end of a growing DNA chain via nucleophilic attack. In the first step of this reaction:
a.The OH group of the incoming nucleotide attacks the 5' triphosphate of the last nucleotide attached to the DNA strand.
b. The OH group of the incoming nucleotide attacks the 5' monophosphate of the last nucleotide attached to the DNA strand.
c. The OH group of the last nucleotide attached to the DNA strand attacks the 5' triphosphate of the incoming nucleotide.
d. The OH group of the last nucleotide attached to the DNA strand attacks the 5' monophosphate of the incoming nucleotide.
2. Nucleotides are added to the 3' end of a growing DNA chain via nucleophilic attack. In the second step of this reaction:
a. A monophosphate is removed from the newly attached nucleotide.
b. A diphosphate is removed from the newly attached nucleotide.
c. A triphosphate is removed from the newly attached nucleotide.
3. Which of the following is necessary for a DNA synthesis reaction catalyzed by DNA polymerase? Select all that apply.
a. Template DNA
b. RNA primer
c.ATP
d. dNTPs
4. DNA polymerases also have nuclease activities. Which of the following is not a use for the nuclease activity of DNA polymerase I?
a. Proofreading during synthesis.
b. Trimming single-stranded ends.
c. Removal of RNA primers.
d. Degradation of viral DNAs.
e. Removal of DNA lesions during repair.
5.
Which of the following correctly describes the roles of Mg2+ ions in the polymerase reaction?
a. The first Mg2+ deprotonates the aspartate in the active site.
b. The first Mg2+ deprotonates the 3' OH of the last nucleotide in the DNA strand.
c. The second Mg2+ protonates an OH group to form water in the active site.
d. The second Mg2+ stabilizes pyrophosphate by protonation.
e. None of the answers.
6. Arthur Kornberg's group found that in vitro DNA replication required all four dNTPs. What conclusion did they arrive at based on this result?
a. An RNA primer must also be needed for synthesis.
b. The DNA synthesis enzyme must be using a DNA strand as a template for synthesis.
c. DNA consists of four bases.
d. In vitro DNA replication differs from in vivo DNA replication.
Explanation / Answer
1. Answer
In replication process, the new DNA strand is synthesized by polymerization reaction. It is catalyzed by the enzyme DNA polymerase. It catalyzes the formation of a phosphodiester bond between two nucleotides. This reaction proceeds in 5’ to 3’ reaction. The upcoming triphosphate nucleotide is bonded to the 3’-hydroxyl group of the growing chain.
Therefore, option c is correct.
2. Answer
The phosphodiester bond is formed between the two nucleotides by the nucleophilic attack. During this bond formation, two phosphate groups are removed from the newly joined nucleotide.
Therefore, option b is correct.
3. Answer
DNA polymerase catalyzes the reaction of DNA synthesis. For this reaction the enzyme requires a primer to which the upcoming nucleotides bind, a template strand for complementary base pairing and the deoxyribonucleotides.
Therefore, options a, b, and d are correct.
4. Answer
DNA polymerase enzyme has exonuclease activity to remove mismatch pairs, DNA repair, degradation of DNA and removal of primers. There are exonuclease enzymes for removing single stranded DNA ends.
Therefore, option b is correct.
5. Answer
DNA polymerase enzyme requires two Mg2+ ions for its activity. This ion binds to the 3’-OH group of the growing chain and stabilizes the oxide ion (O-). It also increase its nucleophile property leading to the nucleophilic attack on the phosphate group of the newly bonding nucleotide. Another ion binds to the diphosphate or pyrophosphate group released, to stabilize its negative charges.
Therefore, options b and d are correct.
6. Answer
Arthur Kornberg’s experiment on DNA replication revealed that the DNA synthesized is biologically active. It requires all four nucleotides for its synthesis. Based on the result they concluded that the synthesized strand must be using the DNA template.
Therefore, option b is correct.
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