Concept explainers
In the following drawing, the top strand is the template DNA, and the bottom strand shows the lagging strand prior to the action of DNA polymerase I. The lagging strand contains three Okazaki fragments. The RNA primers have not yet been removed.
A. Which Okazaki fragment was made first, the one on the left or the one on the right?
B. Which RNA primer will be the first one to be removed by DNA polymerase I, the primer on the left or the primer on the right? For this 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? Explain.
C. Let’s consider how DNA ligase connects the left Okazaki fragment with the middle Okazaki fragment. After DNA polymerase I removes the middle RNA primer and fills in the gap with DNA, where does DNA ligase function? See the arrows on either side of the middle RNA primer. Is ligase needed at the left arrow, at the right arrow, or both?
D. When connecting two Okazaki fragments, DNA ligase uses
or ATP as a source of energy to catalyze this reaction. Explain why DNA ligase needs another source of energy to connect two nucleotides, but DNA polymerase needs nothing more than the incoming
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Chapter 11 Solutions
Genetics: Analysis and Principles
- a. This piece of DNA is cut by EcoRI, the resulting fragments are separated by gel electrophoresis, and the gel is stained with ethidium bromide. Draw a picture of the bands that will appear on the gel. b. If a mutation that alters EcoRI site 1 occurs in this piece of DNA, how will the banding pattern on the gel differ from the one that you drew in part a? c. If mutations that alter EcoRI sites 1 and 2 occur in this piece of DNA, how will the banding pattern on the gel differ from the one that you drew in part a? d. If 1000 bp of DNA were inserted between the two restriction sites, how would the banding pattern on the gel differ from the one that you drew in part a? e. If 500 bp of DNA between the two restriction sites were deleted, how would the banding pattern on the gel differ from the one that you drew in part a?arrow_forwardThe figure at the right shows a partially drawn replication fork. a) Annotate this figure to show the proper location of each of the following: • template DNA strand polarity • DNA polymerase I Topoisomerase (gyrase) • leading strand daughter fragment(s) lagging strand daughter fragment(s) Single stranded binding proteins • DNA polymerase III • Primase • Ligase • Helicasearrow_forwardIn the drawing shown below, the top strand (purple) is the template DNA, and the bottom shows the synthesis of the lagging strand (DNA in blue and RNA primers in red). 3' 5" ыш Left Okazaki fragment --- -11-- Middle Okazaki fragment Right Okazaki fragment 5' 3' After DNA polymerase I removes the middle primer and fills in with DNA, where is DNA ligase needed? See the arrows on both sides of the middle primer. Explain whether ligase is needed at the left arrow, at the right arrow, or both?arrow_forward
- You are studying a colony of cells and determine that some of these cells have a mutated DNA polymerase I that results in loss of function of this enzyme. A) What will the effect of the mutation in DNA polymerase I be on DNA replication? In your answer make sure to describe what would be observed in the leading and lagging strand and explain your reasoning. B) Will this mutation in DNA polymerase I have an impact on another step in DNA replication? In your answer make sure to indicate whether DNA replication will be impacted or not. If it is not, explain why. If it is impacted, then describe the step that is impacted and name the molecule or enzyme involved.arrow_forwardDoes the addition of a histidine tag affect DNA polymerase activity and or processivity? Give a detailed explanation.arrow_forwardIn DNA replication, RNA primase is used to construct primers which are complementary to the DNA strand. In PCR we include primers that flanks (sits down on either side) the area of the genome we want amplified. A primer is needed in order for DNA polymerase to start the replication process (making covalent bonds between nucleotides). Specifically, why is the primer needed in order for DNA ploymerase to start synthesis? A ) primers provide the free OH group needed by DNA polymerase to make the first covalent bond B) to prevent DNA helicase from breaking too many H bonds C) the DNA is in danger of becoming denatured without a primer D) primers provide the free phosphate group needed by DNA polymerase to make the first covalent bond E) primers will provide enough energy to help the reaction occurarrow_forward
- Adenylate cyclase, which synthesizes cyclic AMP from ATP, requires two metal ions, and the enzyme has the same constellation of amino acid residues in the active site as does DNA polymerase I. In what sense is the adenylate cyclase reaction similar to that of DNA polymerase, and in what sense is it different?arrow_forwardYou used agarose gel electrophoresis to separate DNA fragments of different size and the experiment worked well. However, you wanted to re run the experiment but this time you made the gel with a higher percentage of Agarose. How might this affect your results compared to the first run? a. There would be no difference between the runs since it is the current, not the agarose that causes migration. b. The higher concentration of agarose would cause the DNA to break apart. c. You can't predict how the concetration of agarose would affect migration. d. The DNA fragments would migrate further down the gel than they did the first time. e. The DNA fragments wouldn't migrate as far down the gel as they did the first time.arrow_forwardWhich of these two changes is more difficult for DNA repair enzymes to fix correctly? Explain why.arrow_forward
- What is an Okazaki fragment? In which strand of replicating DNA are Okazaki fragments found? Based on the properties of DNA polymerase, why is it necessary to make these fragments?arrow_forwardDNA polymerase I has 5'-3' polymerase activity, 5'-3' exonuclease activity, and 3'-5' exonuclease activity necessary for DNA replication. Mutations in the gene that encodes DNA polymerase I may cause the enzyme to lose these activities. Match the consequence of a loss-of-function mutation in DNA polymerase I to the corresponding lost activity. Lost 5'-3' polymerase activity no RNA primer removal during DNA replication no double helix denaturation Lost 5'-3' exonuclease activity Answer Bank decreased polymerase fidelity Lost 3'-5' exonuclease activity no DNA synthesis to fill gaps caused by removing RNA primers unstable strand separation within the replication bubblearrow_forwardSingle-strand binding proteins keep the two parental strands of DNA separated from each other until DNA polymerase has an opportunity to replicate the strands. Suggest how single-strand binding proteins keep the strands separated and yet do not impede the ability of DNA polymerase to replicate the strands.arrow_forward
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