DNA Structure And Replication Sample Questions

1. A sample of human DNA is subjected to increasing temperature until the major fraction exhibits optical density changes due to disruption of its helix (melting or denaturation). A smaller fraction is atypical in that it requires a much higher temperature for melting. The smaller, atypical fraction of DNA must contain a higher content of

Adenine plus cytosine

Cytosine plus guanine

Adenine plus thymine

Cytosine plus thymine

Adenine plus guanine

The smaller, atypical fraction of DNA requiring a higher temperature for melting suggests that it has a higher content of Cytosine plus Guanine. Cytosine and Guanine form three hydrogen bonds with each other, making their bond stronger compared to the two hydrogen bonds formed between Adenine and Thymine. This stronger bond requires a higher temperature to break, resulting in a higher melting point for the DNA fraction with a higher content of Cytosine plus Guanine.

Explanation

The smaller, atypical fraction of DNA requiring a higher temperature for melting suggests that it has a higher content of Cytosine plus Guanine. Cytosine and Guanine form three hydrogen bonds with each other, making their bond stronger compared to the two hydrogen bonds formed between Adenine and Thymine. This stronger bond requires a higher temperature to break, resulting in a higher melting point for the DNA fraction with a higher content of Cytosine plus Guanine.

2. It is well know that DNA polymerases synthesize DNA only in the 5' to 3' direction. Yet, at the replication fork, both strands of parental DNA are being replicated with the synthesis of new DNA. How is it possible that while one strand is being synthesized in the 5' to 3' direction, the other strand appears to be synthesized in the 3' to 5' direction? This apparent paradox is explained by

3’ to 5’ DNA repair enzymes

3’ to 5’ DNA polymerase

Okazaki fragments

Replication and immediate crossover of the leading strand

Lack of RNA primers on one of the strands

Okazaki fragments are short, discontinuous stretches of DNA that are synthesized on the lagging strand during DNA replication. They are synthesized in the 5' to 3' direction by DNA polymerase, just like the leading strand. However, due to the antiparallel nature of DNA, the lagging strand is oriented in the opposite direction, necessitating the synthesis of Okazaki fragments in the opposite direction. These fragments are later joined together by DNA ligase to form a continuous strand. Therefore, the presence of Okazaki fragments explains how both strands of parental DNA can be replicated in the 5' to 3' direction.

Explanation

Okazaki fragments are short, discontinuous stretches of DNA that are synthesized on the lagging strand during DNA replication. They are synthesized in the 5' to 3' direction by DNA polymerase, just like the leading strand. However, due to the antiparallel nature of DNA, the lagging strand is oriented in the opposite direction, necessitating the synthesis of Okazaki fragments in the opposite direction. These fragments are later joined together by DNA ligase to form a continuous strand. Therefore, the presence of Okazaki fragments explains how both strands of parental DNA can be replicated in the 5' to 3' direction.

3. Which of the following statements regarding a double-helical molecule of DNA is true?

All hydroxyl groups of pentoses are involved in linkages

Bases are perpendicular to the axis

Each strand is identical

Each strand has parallel, 5’ to 3’ direction

Each strand replicates itself

The statement that bases are perpendicular to the axis is true for a double-helical molecule of DNA. In the DNA structure, the two strands of the double helix are held together by hydrogen bonds between the bases. The bases are stacked on top of each other and form pairs, with adenine (A) always pairing with thymine (T), and guanine (G) always pairing with cytosine (C). These base pairs are perpendicular to the axis of the helix, creating the characteristic twisted ladder shape of DNA.

Explanation

The statement that bases are perpendicular to the axis is true for a double-helical molecule of DNA. In the DNA structure, the two strands of the double helix are held together by hydrogen bonds between the bases. The bases are stacked on top of each other and form pairs, with adenine (A) always pairing with thymine (T), and guanine (G) always pairing with cytosine (C). These base pairs are perpendicular to the axis of the helix, creating the characteristic twisted ladder shape of DNA.

4. If a completely radioactive double-stranded DNA molecule undergoes two rounds of replication in a solution free of radioactive label, what is the radioactivity status of the resulting four double-stranded DNA molecules?

Half should contain no radioactivity

All should contain radioactivity

Half should contain radioactivity in both strands

One should contain radioactivity in both strands

None should contain radioactivity

When a completely radioactive double-stranded DNA molecule undergoes replication, each strand acts as a template for the synthesis of a new complementary strand. In the first round of replication, the resulting two double-stranded DNA molecules will have one radioactive strand and one non-radioactive strand. In the second round of replication, each of these molecules will again act as a template, resulting in four double-stranded DNA molecules. Since the solution is free of radioactive label, the newly synthesized strands in the second round will not be radioactive. Therefore, half of the resulting four double-stranded DNA molecules will contain no radioactivity.

Explanation

When a completely radioactive double-stranded DNA molecule undergoes replication, each strand acts as a template for the synthesis of a new complementary strand. In the first round of replication, the resulting two double-stranded DNA molecules will have one radioactive strand and one non-radioactive strand. In the second round of replication, each of these molecules will again act as a template, resulting in four double-stranded DNA molecules. Since the solution is free of radioactive label, the newly synthesized strands in the second round will not be radioactive. Therefore, half of the resulting four double-stranded DNA molecules will contain no radioactivity.

5. A child presents with severe growth failure, accelerated aging that causes adult complications such as diabetes and coronary artery disease, and microcephaly (small head) due to increased nerve cell death. In vitro assay of labeled thymidine incorporation reveals decreased levels of DNA synthesis compared to controls, but normal-sized labeled DNA fragments. The addition of protein extract from normal cells, gently heated to inactivate DNA polymerase, restores DNA synthesis in the child's cell extracts to normal. Which of the enzymes used in DNA replication is likely to be defective in this child?

DNA-directed DNA polymerase

Unwinding proteins

DNA polymerase I

DNA-directed RNA polymerase

DNA ligase

The child's symptoms suggest a defect in DNA replication, as indicated by the decreased levels of DNA synthesis. The fact that the addition of protein extract from normal cells restores DNA synthesis suggests that a specific enzyme is likely defective in the child. Unwinding proteins are responsible for separating the DNA strands during replication, allowing DNA polymerase to access the template strand and synthesize new DNA. Therefore, a defect in unwinding proteins would impair DNA replication and explain the symptoms observed in the child.

Explanation

The child's symptoms suggest a defect in DNA replication, as indicated by the decreased levels of DNA synthesis. The fact that the addition of protein extract from normal cells restores DNA synthesis suggests that a specific enzyme is likely defective in the child. Unwinding proteins are responsible for separating the DNA strands during replication, allowing DNA polymerase to access the template strand and synthesize new DNA. Therefore, a defect in unwinding proteins would impair DNA replication and explain the symptoms observed in the child.

6. Which of the following statements correctly describes eukaryotic nuclear chromosomal DNA?

Each discontinuous piece making up the chromosomes of eukaryotes is about the same size as each prokaryotic chromosome

Unlike bacterial DNA, no histones are associated with it

It is not replicated semiconservatively

It is a linear and unbranched molecule

It is not associated with a specific membranous organelle

The correct answer states that eukaryotic nuclear chromosomal DNA is a linear and unbranched molecule. This means that the DNA in eukaryotic cells is organized into a linear structure, unlike prokaryotic DNA which is circular. Additionally, the DNA is not associated with a specific membranous organelle.

Explanation

The correct answer states that eukaryotic nuclear chromosomal DNA is a linear and unbranched molecule. This means that the DNA in eukaryotic cells is organized into a linear structure, unlike prokaryotic DNA which is circular. Additionally, the DNA is not associated with a specific membranous organelle.

7. Which of the following descriptions of DNA replication is not common to the synthesis of both leading and lagging strands?

RNA primer is synthesized

DNA polymerase III synthesizes DNA

Helicase (rep protein) continuously unwinds duplex DNA at the replication fork during synthesis

Nucleoside monophosphates are added in a 5’ to 3’ direction along the growing DNA chain

DNA ligase repeatedly joins the ends of DNA along the growing strand

The synthesis of both the leading and lagging strands involves the synthesis of an RNA primer, where a short segment of RNA is synthesized to provide a starting point for DNA synthesis. DNA polymerase III is responsible for synthesizing DNA in both strands. Helicase continuously unwinds the duplex DNA at the replication fork during synthesis, allowing the DNA polymerase to access the separated strands. Nucleoside monophosphates are added in a 5' to 3' direction along the growing DNA chain, which is a characteristic feature of DNA replication. However, DNA ligase is only involved in the lagging strand synthesis, where it joins the Okazaki fragments together. Therefore, the statement that DNA ligase repeatedly joins the ends of DNA along the growing strand is not common to the synthesis of both leading and lagging strands.

Explanation

The synthesis of both the leading and lagging strands involves the synthesis of an RNA primer, where a short segment of RNA is synthesized to provide a starting point for DNA synthesis. DNA polymerase III is responsible for synthesizing DNA in both strands. Helicase continuously unwinds the duplex DNA at the replication fork during synthesis, allowing the DNA polymerase to access the separated strands. Nucleoside monophosphates are added in a 5' to 3' direction along the growing DNA chain, which is a characteristic feature of DNA replication. However, DNA ligase is only involved in the lagging strand synthesis, where it joins the Okazaki fragments together. Therefore, the statement that DNA ligase repeatedly joins the ends of DNA along the growing strand is not common to the synthesis of both leading and lagging strands.

8. Which of the following enzymes can be described as a DNA-dependent RNA polymerase?

Primase

DNA ligase

DNA gyrase

RNA polymerase III

Reverse transcriptase

A and D are both correct answers

Explanation

A and D are both correct answers

9. Mammalian chromosomes have specialized structures with highly repetitive DNA at their ends (telomeres). Which aspect of telomeric DNA replication is different from that of other chromosomal regions?

The DNA polymerase uses an RNA primer but does not degrade it

The DNA polymerase contains an RNA molecule that serves as template for DNA synthesis

The DNA polymerase must cross-link the 5’ and 3’ termini

The DNA polymerase has a  subunit that facilitates binding to repetitive DNA

The DNA polymerase does not use an RNA template or primer

The correct answer is that the DNA polymerase contains an RNA molecule that serves as a template for DNA synthesis. This means that the DNA polymerase uses the RNA molecule as a guide to synthesize the DNA strand. This is different from other chromosomal regions where DNA polymerase uses an RNA primer but does not degrade it, or where the DNA polymerase must cross-link the 5’ and 3’ termini. It is also different from the situation where the DNA polymerase has a σ subunit that facilitates binding to repetitive DNA. In the case of telomeric DNA replication, the DNA polymerase uses an RNA molecule as a template for DNA synthesis.

Explanation

The correct answer is that the DNA polymerase contains an RNA molecule that serves as a template for DNA synthesis. This means that the DNA polymerase uses the RNA molecule as a guide to synthesize the DNA strand. This is different from other chromosomal regions where DNA polymerase uses an RNA primer but does not degrade it, or where the DNA polymerase must cross-link the 5’ and 3’ termini. It is also different from the situation where the DNA polymerase has a σ subunit that facilitates binding to repetitive DNA. In the case of telomeric DNA replication, the DNA polymerase uses an RNA molecule as a template for DNA synthesis.