- Bacteria are grown in a medium containing a heavy isotope of nitrogen (¹⁵N) for many generations. They are then transferred to a medium containing a light isotope (¹⁴N) and allowed to replicate exactly twice. After these two rounds of replication, what percentage of the DNA molecules will contain at least one strand of ¹⁵N?
Answer: 50%
After the first replication in ¹⁴N medium, all DNA molecules are hybrids (¹⁵N-¹⁴N). After the second replication, these two hybrid molecules replicate. Each produces one new hybrid molecule and one entirely light (¹⁴N-¹⁴N) molecule. This results in a total of four DNA molecules: two are hybrid and two are light. Therefore, 2 out of 4 molecules, or 50%, contain at least one ¹⁵N strand.
- During DNA replication, the leading strand is synthesized continuously while the lagging strand is synthesized discontinuously. Which statement best explains this difference?
Answer: The leading strand template allows DNA polymerase to move in the same direction as the replication fork, while the lagging strand template does not.
The core reason is the antiparallel nature of DNA and the unidirectional 5' to 3' synthesis activity of DNA polymerase. The replication fork unwinds in one direction. The leading strand template is oriented such that DNA polymerase can follow the fork continuously. The lagging strand template is oriented in the opposite direction, forcing the polymerase to synthesize away from the fork in short fragments.
- Which of the following events in DNA replication occurs first?
Answer: Helicase breaks hydrogen bonds between base pairs.
DNA replication must begin with the separation of the two parent strands. This is accomplished by helicase, which unwinds the double helix by breaking the hydrogen bonds between complementary bases. Only after the strands are separated can primase create a primer (D), and then DNA polymerase can begin adding nucleotides (A). Joining of Okazaki fragments by ligase (B) occurs later in the process on the lagging strand.
- What is the primary role of the proofreading function of DNA polymerase?
Answer: To detect and remove incorrectly paired nucleotides immediately after their insertion.
The proofreading function, typically an exonuclease activity of the DNA polymerase enzyme itself, acts as a quality control mechanism. It checks each newly added nucleotide against the template. If a mismatch is detected, the polymerase removes the incorrect nucleotide and inserts the correct one, greatly increasing the fidelity of DNA replication.
- A hypothetical drug is developed that allows DNA polymerase to synthesize in both the 5' to 3' and 3' to 5' directions. If this drug were applied to a dividing cell, what would be the most likely outcome for DNA replication? [HL]
Answer: Both the leading and lagging strands would be synthesized continuously.
The entire reason for discontinuous synthesis and Okazaki fragments on the lagging strand is the strict 5' to 3' directionality of DNA polymerase. If the polymerase could synthesize in the 3' to 5' direction as well, it could simply follow the replication fork along both template strands, synthesizing both new strands continuously. This would eliminate the need for Okazaki fragments and the action of DNA ligase.
- In the process of DNA replication, what is the functional relationship between helicase and DNA polymerase?
Answer: Helicase unwinds the DNA, providing single-stranded templates for DNA polymerase to copy.
The two enzymes have sequential roles. Helicase moves along the DNA, separating the two strands to create a replication fork. This action exposes the nucleotide bases on each strand, creating single-stranded templates. DNA polymerase then uses these templates to synthesize the new complementary strands. The other options misrepresent the roles: primase makes primers, polymerase itself proofreads, and initiation is controlled by initiator proteins, not polymerase.
- The sequence of events for synthesizing a portion of the lagging strand is: 1. DNA ligase joins fragments. 2. Primase adds an RNA primer. 3. Helicase unwinds DNA. 4. DNA polymerase synthesizes a DNA fragment. What is the correct chronological order of these events? [HL]
Answer: 3, 2, 4, 1
The correct sequence starts with the unwinding of the DNA template by helicase (3). Once a single-stranded region is available, primase must synthesize an RNA primer to provide a starting point (2). DNA polymerase then extends this primer, synthesizing a short DNA fragment (an Okazaki fragment) (4). Finally, after multiple fragments are made and primers are replaced, DNA ligase joins the adjacent fragments to create a continuous strand (1).
- During which phase of the cell cycle does DNA replication occur in eukaryotes?
Answer: S phase of interphase
The cell cycle is divided into interphase (G1, S, and G2) and the M phase (mitosis and cytokinesis). DNA replication, or synthesis, occurs specifically during the S phase of interphase. The purpose is to create an identical copy of the genome, resulting in chromosomes composed of two sister chromatids, in preparation for cell division.
- Okazaki fragments are a feature of DNA replication. Which combination of enzymes is required to produce a continuous strand of DNA from these fragments? [HL]
Answer: DNA polymerase and DNA ligase
After primase creates RNA primers and DNA polymerase synthesizes the short DNA fragments (Okazaki fragments), two steps are needed to create a continuous strand. First, a type of DNA polymerase removes the RNA primers and replaces them with DNA nucleotides. Second, DNA ligase forms the final phosphodiester bond that joins the adjacent fragments together. Therefore, both DNA polymerase (for primer replacement) and DNA ligase (for joining) are essential.
- The 'end-replication problem' in eukaryotes refers to the progressive shortening of linear chromosomes with each cell division. Which statement accurately describes the underlying cause of this problem? [HL]
Answer: The removal of the final RNA primer on the lagging strand leaves a gap that cannot be filled by DNA polymerase.
On the lagging strand, synthesis requires RNA primers. When the final primer at the 5' end of the newly synthesized strand is removed, there is no existing 3'-OH group for DNA polymerase to add nucleotides to. Consequently, this gap is not filled, and the chromosome becomes shorter with each round of replication. This shortening occurs at the telomeres.
- A scientist is studying a DNA molecule where one strand has the base sequence 5'-AGCTTCG-3'. What will be the sequence of the complementary strand synthesized during replication?
Answer: 3'-TCGAAGC-5'
DNA strands are antiparallel. The complementary strand will run in the opposite direction (3' to 5'). Base pairing rules are A with T, and G with C. Therefore, the complementary sequence to 5'-AGCTTCG-3' is 3'-TCGAAGC-5'. Choice A is incorrect because it has the wrong directionality (5' to 3') although the bases are complementary. Choice B is incorrect because it contains uracil (U), which is found in RNA, not DNA. Choice C has the correct bases but is written in the wrong direction.
- DNA replication is described as semi-conservative because each new DNA molecule formed consists of:
Answer: one original parental strand and one newly synthesized daughter strand.
The term 'semi-conservative' means that half of the original molecule is conserved in each of the two new molecules. Specifically, the parental double helix unwinds, and each of its strands serves as a template for a new complementary strand. The result is two identical DNA molecules, each composed of one old (parental) strand and one new (daughter) strand.
- Which statement correctly distinguishes DNA replication in prokaryotes from that in eukaryotes?
Answer: Prokaryotic replication proceeds from a single origin of replication, while eukaryotic replication begins at multiple origins.
Prokaryotes typically have a single, circular chromosome and initiate replication from one origin of replication. Eukaryotes have large, linear chromosomes and must initiate replication at multiple origins simultaneously to complete the process in a timely manner. Both systems involve leading/lagging strands, require primers, and have polymerases that synthesize in the 5' to 3' direction.
- The energy required to form the phosphodiester bond between an incoming nucleotide and the growing DNA strand is supplied by which of the following?
Answer: The hydrolysis of the two terminal phosphate groups from the incoming deoxynucleoside triphosphate.
The building blocks for DNA synthesis are deoxynucleoside triphosphates (e.g., dATP, dGTP). These molecules carry their own energy. When DNA polymerase adds a nucleotide to the growing chain, it cleaves off the two terminal phosphate groups (pyrophosphate). The hydrolysis of this high-energy phosphate bond provides the energy to drive the formation of the phosphodiester bond.
- A researcher uses a drug that specifically inhibits the function of DNA ligase in a culture of dividing eukaryotic cells. Which of the following would be the most direct consequence for DNA synthesis?
Answer: Synthesis of the leading strand would be unaffected, but the lagging strand would consist of unjoined fragments.
DNA ligase is responsible for joining the Okazaki fragments on the lagging strand by forming phosphodiester bonds. Its inhibition would not affect the unwinding of DNA (helicase), the synthesis of primers (primase), or the continuous synthesis of the leading strand. It would, however, prevent the fragments of the discontinuously synthesized lagging strand from being joined into a single continuous strand.
- If a mutation rendered the enzyme primase non-functional in a cell, what would be the immediate effect on DNA replication?
Answer: The parent DNA strands would separate, but polymerization of new strands would not begin.
Primase synthesizes short RNA primers that provide a necessary 3'-OH group for DNA polymerase to begin synthesis. Without functional primase, no primers can be laid down on either the leading or the lagging strand. Helicase can still unwind the DNA, but DNA polymerase cannot initiate synthesis of new strands, halting the entire process after unwinding.
- Which statement correctly describes the formation of chemical bonds during DNA replication?
Answer: DNA polymerase forms phosphodiester bonds, and hydrogen bonds form between complementary bases.
During replication, DNA polymerase catalyzes the formation of phosphodiester bonds to create the sugar-phosphate backbone of the new strand. Hydrogen bonds form spontaneously between the complementary base pairs (A-T and G-C) without enzymatic action. Helicase breaks, not forms, hydrogen bonds. DNA ligase forms phosphodiester bonds, not hydrogen bonds.
- A cell is exposed to a chemical agent that prevents hydrogen bonds from forming between cytosine and guanine, but not between adenine and thymine. How would this affect DNA replication?
Answer: Replication would proceed, but with a very high error rate specifically at G-C base pairs.
Hydrogen bonds are crucial for the specificity of base pairing. If C cannot properly bond with G, DNA polymerase might incorrectly insert A or T opposite a G on the template strand, or vice-versa. This would dramatically increase the mutation rate. Replication would still proceed because A-T bonds would form, and the polymerase would still create the phosphodiester backbone, but the fidelity would be severely compromised at G-C sites.
- The synthesis of the lagging strand during DNA replication is discontinuous. What is the fundamental reason for this discontinuity? [HL]
Answer: DNA polymerase can only synthesize new DNA in a 5' to 3' direction, which is opposite to the direction of the replication fork's movement for the lagging strand.
DNA polymerase has a strict structural requirement: it can only add nucleotides to the 3' end of a growing strand, meaning synthesis always proceeds in the 5' to 3' direction. As the replication fork unwinds, the leading strand can be synthesized continuously in the same direction. However, the lagging strand template runs in the opposite direction, so it must be synthesized discontinuously in short segments (Okazaki fragments) that are individually made in the 5' to 3' direction.
