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Ch. 11 - DNA Replication and Recombination
Chapter 11, Problem 27

DNA polymerases in all organisms add only 5' nucleotides to the 3' end of a growing DNA strand, never to the 5' end. One possible reason for this is the fact that most DNA polymerases have a proofreading function that would not be energetically possible if DNA synthesis occurred in the 3' to 5' direction. Sketch the reaction that DNA polymerase would have to catalyze if DNA synthesis occurred in the 3' to 5' direction.

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1
Identify the normal direction of DNA synthesis, which is 5' to 3'.
Understand that DNA polymerase adds nucleotides to the 3' end of the growing DNA strand.
Consider the reverse scenario where synthesis occurs in the 3' to 5' direction.
Sketch the reaction: In this hypothetical scenario, the incoming nucleotide would need to be added to the 5' end of the growing strand.
Note that this would require a different mechanism for proofreading, as the energy for proofreading comes from the hydrolysis of the triphosphate group of the incoming nucleotide, which is not feasible in the 3' to 5' direction.

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Key Concepts

Here are the essential concepts you must grasp in order to answer the question correctly.

DNA Polymerase Function

DNA polymerases are enzymes responsible for synthesizing new DNA strands by adding nucleotides to the 3' end of a growing chain. This unidirectional synthesis is crucial for maintaining the integrity of the genetic code and ensuring accurate replication. The enzyme catalyzes the formation of phosphodiester bonds between nucleotides, which is essential for DNA strand elongation.
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Directionality of DNA Synthesis

DNA synthesis occurs in a 5' to 3' direction, meaning that nucleotides are added to the 3' hydroxyl group of the last nucleotide in the chain. This directionality is fundamental to the structure of DNA and the mechanisms of replication and transcription. If synthesis were to occur in the 3' to 5' direction, it would disrupt the established biochemical pathways and the energetics of nucleotide addition.
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Proofreading Mechanism

Many DNA polymerases possess a proofreading function that allows them to correct errors during DNA synthesis. This function relies on the enzyme's ability to detect mismatched nucleotides and excise them before continuing synthesis. If DNA synthesis occurred in the 3' to 5' direction, the proofreading mechanism would be less efficient and energetically unfavorable, potentially leading to increased mutation rates.
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Related Practice
Textbook Question
The genome of D. melanogaster consists of approximately 1.7x10⁸ base pairs. DNA synthesis occurs at a rate of 30 base pairs per second. In the early embryo, the entire genome is replicated in five minutes. How many bidirectional origins of synthesis are required to accomplish this feat?
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Textbook Question
Assume a hypothetical organism in which DNA replication is conservative. Design an experiment similar to that of Taylor, Woods, and Hughes that will unequivocally establish this fact. Using the format established in Figure 11.5, draw sister chromatids and illustrate the expected results establishing this mode of replication.
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Textbook Question
At the end of the short arm of human chromosome 16 (16p), several genes associated with disease are present, including thalassemia and polycystic kidney disease. When that region of chromosome 16 was sequenced, gene-coding regions were found to be very close to the telomere-associated sequences. Could there be a possible link between the location of these genes and the presence of the telomere-associated sequences? What further information concerning the disease genes would be useful in your analysis?
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Textbook Question
DNA polymerases in all organisms add only 5' nucleotides to the 3' end of a growing DNA strand, never to the 5' end. One possible reason for this is the fact that most DNA polymerases have a proofreading function that would not be energetically possible if DNA synthesis occurred in the 3' to 5' direction. Consider the information in your sketch and speculate as to why proofreading would be problematic.
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Textbook Question
Assume that the sequence of bases shown below is present on one nucleotide chain of a DNA duplex and that the chain has opened up at a replication fork. Synthesis of an RNA primer occurs on this template starting at the base that is underlined. If the RNA primer consists of eight nucleotides, what is its base sequence?
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Textbook Question
Assume that the sequence of bases shown below is present on one nucleotide chain of a DNA duplex and that the chain has opened up at a replication fork. Synthesis of an RNA primer occurs on this template starting at the base that is underlined. In the intact RNA primer, which nucleotide has a free 3'-OH terminus? 3'.......GGCTACCTGGATTCA....5'
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