Chapter 6 - DNA Replication and Repair
If a stretch of DNA on the parental strand of a replicating chromosome has the sequence 5ʹ-AGCTCGATCGGCTA-3ʹ, what will the sequence of the newly synthesized strand made from this stretch of template be? Choose one: 3ʹ-TCGAGCTAGCCGAT-5ʹ 5ʹ-AGCTCGATCGGCTA-3ʹ 5ʹ-TCGAGCTAGCCGAT-3ʹ 3ʹ-AGCTCGATCGGCTA-5ʹ
3ʹ-TCGAGCTAGCCGAT-5ʹ The parental strand will be used as a template for replication using complementary base pairing rules. So, the new strand will be complementary and antiparallel to the other.
The nucleotide sequence of one DNA strand in a DNA double helix is 5'-CATTGCCAGAAAAAT-3'. What is the sequence of the complementary strand produced during replication? Choose one: 5'-GTAACGGTCTTTTTA-3' 5'-CATTGCCAGAAAAAT-3' 5'-TAAAAAGACCGTTAC-3' 5'-GATTCGGAGTTTTTA-3' 5'-ATTTTTCTGGCAATG-3'
5'-ATTTTTCTGGCAATG-3' 5'-ATTTTTCTGGCAATG-3' is the complement to 5'-CATTGCCAGAAAAAT-3'. DNA is always written 5' to 3' if single stranded. When DNA is double stranded and is being written to show double strandedness, then the complement is written below and can be written 3' to 5' to demonstrate antiparallel double strandedness. A strand of DNA does not have the same sequence as its complement; rather, complementary DNA strands run antiparallel to one another. Therefore, the complementary strand must have the opposite polarity.
What powers the action of helicase at the replication fork, where it opens up the double helix? Choose one: A. ATP hydrolysis B. DNA hydrolysis C. DNA synthesis D. the attachment of single-strand DNA-binding proteins to the lagging-strand template E. pyrophosphate hydrolysis
A. ATP hydrolysis Correct. Helicases use the energy of ATP hydrolysis to move forward along the DNA, prying apart the double helix as it progresses.
The DNA helicase animation shows the bacteriophage T7 helicase unwinding DNA. Which of the following are critical components of the helicase mechanism of action necessary to unwind DNA? Choose one or more: A. conformational changes of subunits B. oscillating loops pulling the single-stranded DNA through a central hole C. ATP binding and hydrolysis D. binding of four helicase subunits to the double-stranded DNA E. dissociation of the helicase subunits
A. conformational changes of subunits B. oscillating loops pulling the single-stranded DNA through a central hole C. ATP binding and hydrolysis Correct. Six helicase subunits go through cycles of ATP binding and hydrolysis to change conformation. The conformational changes lead to a pulling of the single-stranded DNA through the central hole.
Which of the following does not cause a mutation? Choose one: A. evolution B. replication errors C. UV radiation D. failure of DNA repair systems E. metabolic activity
A. evolution Correct. Evolution by means of natural selection is dependent upon variation in the genetic makeup of populations, which results from mutation. However, mutations arise independently through a number of different mechanisms. Mutations can arise spontaneously as a result of exposure to harmful conditions or as a result of defects in DNA replication and repair machinery. Any mutations that are not repaired will fall into one of three categories: beneficial, harmful, or neutral (meaning they pose no harm or benefit to the individual). A mutation that is harmful will be selected against and be removed from the population. In contrast, those that are beneficial will confer a survival advantage and not only persist, but become more prevalent in successive generations of the population. This process of preferential survival based on the particular variant of a gene that an individual harbors is the basis of evolution. Therefore, evolution acts upon mutations that arise in a population, but is not the cause of the mutation itself.
What type of enzyme seals the newly added (repaired) DNA to the rest of the DNA molecule? Choose one: A. ligase B. helicase C. DNase D. primase E. polymerase
A. ligase Correct. Ligases join DNA fragments by catalyzing the formation of phosphodiester bonds. Ligases join DNA fragments by catalyzing the formation of phosphodiester bonds between them, during both DNA replication and mismatch repair. During replication, ligase joins the individual Okazaki fragments together on the lagging strand. During mismatch repair, ligase links the newly inserted nucleotide to the rest of the strand. While similar to DNA polymerase in its ability to form phosphodiester bonds, ligase is different in that it doesn't add free nucleotides to the end of a growing strand of DNA; rather, it links together nicks in the backbone of existing DNA molecules.
Which double-strand break repair mechanism is a simple ligation mechanism? Choose one: A. nonhomologous end joining B. DNA ligase C. homologous recombination D. DNA mismatch repair
A. nonhomologous end joining Nonhomologous end joining is a mechanism for sealing DNA double-strand breaks using DNA ligase. Homologous recombination is more complicated, with end processing and copying of the damaged region from an intact copy of that sequence.
Where does DNA synthesis always begin? Choose one: A. replication origins B. ATG C. the centromere D. CpG islands E. the telomeres
A. replication origins Correct. DNA synthesis begins at replication origins. Human chromosomes contain hundreds of replication origins.
The sequence at which DNA replication begins tends to have which characteristic? Choose one: AT-rich GC-rich G-rich A-rich
AT-rich Replication origins tend to be very rich in A-T base pairs to facilitate local strand separation by initiator proteins.
Which of the following is a function of the protein component of chromosomes? Choose one: A. It helps to translate the genetic message. B. It packages the DNA strands. C. It contains the enzymes that replicate the DNA. D. It carries a portion of the genetic information.
B. It packages the DNA strands. Chromosomes are made up of protein and DNA. The DNA carries the genetic information, and the protein component helps store the long DNA molecules in the cell, in addition to controlling access to the DNA molecules.
What is the function of a topoisomerase in DNA replication? Choose one: A. It binds the template DNA to hold in place. B. It relieves the tension in DNA strands. C. It separates the DNA strands. D. It coils the DNA for tighter packaging.
B. It relieves the tension in DNA strands. Unwinding of the DNA by helicase produces tension in the DNA molecule because the DNA cannot freely rotate. Topoisomerases cut the DNA to allow the DNA to freely rotate and relieve this tension, avoiding supercoils and tangles, and then reseals the DNA.
In bacteria, how does the cell recognize which strand is the newly synthesized strand and thus contains the mismatch? Choose one: A. The newly synthesized strand is methylated. B. The newly synthesized strand is unmethylated. C. The sequence on the newly synthesized strand is made of RNA. D. The sequences on both strands are cut.
B. The newly synthesized strand is unmethylated. In bacterial DNA, adenine bases are methylated. This occurs slowly, so newly synthesized strands remain unmethylated for a time after replication and gives mismatch repair enzymes time to recognize the damaged strand.
What is the function of single-strand binding proteins in DNA replication?Choose one: A. They strip away used RNA primers. B. They bind to regions of DNA, preventing them from forming base pairs together. C. They bind to single-stranded DNA and scan for replication errors. D. They release completed Okazaki fragments. E. They break a DNA double helix to form two separate single strands.
B. They bind to regions of DNA, preventing them from forming base pairs together. Correct. This action keeps the single-stranded DNA in an elongated form that can serve as an efficient template.
What is the name of the type of damage caused by an improperly paired base in the DNA? Choose one: A. depurination B. mismatch C. double-strand break D. thymine dimer
B. mismatch Sometimes mispaired bases escape the proofreading of DNA polymerase during replication. These are called mismatches and can be repaired after replication is complete.
In the absence of repair, what would the replication of a double helix containing a mismatch yield? Choose one: A. two DNA molecules with a mutated sequence B. one DNA molecule with the normal sequence and one DNA molecule with a mutated sequence C. one DNA molecule with the normal sequence and one DNA molecule with a mismatch D. two DNA molecules containing different mismatches at the site of the original error E. two DNA molecules containing the mismatch
B. one DNA molecule with the normal sequence and one DNA molecule with a mutated sequence Correct. In the absence of repair, replication of a double helix containing a mismatch would yield one DNA molecule with the normal sequence and one DNA molecule with a mutated sequence. The mutation in one of the daughter DNA molecules will be permanent and hence replicated each time that DNA molecule is copied. In the absence of repair, following replication, neither daughter DNA molecule will contain the original mismatch, but one will have a mutated sequence that does not match the original parent sequence. Thus, replication of a double helix containing a mismatch would yield one DNA molecule with the normal sequence and one DNA molecule with a mutated sequence. The mutation in one of the daughter DNA molecules will be permanent and hence replicated each time that DNA molecule is copied
Which of the following is NOT a common source of DNA damage for cells in our bodies? Choose one: A. spontaneous loss of amino groups on cytosine B. soap C. replication fork problems D. UV light
B. soap DNA damage can be caused by many sources including UV light, mutagenic chemicals, and radiation (which are all external to the cell), as well as replication fork issues. Soap is not considered a harmful chemical.
In a DNA double helix, which strand serves as the template during replication? Choose one: A. the strand that encodes a protein B. the strand that runs in the 5'-to-3' direction C. Both strands serve as templates during replication. D. the strand that runs in the 3'-to-5' direction E. the strand that is richer in A and T nucleotides
C. Both strands serve as templates during replication. Correct. Regardless of its composition, each strand in a double helix serves as a template during replication.
AMP-PNP is a non-hydrolyzable analog of ATP that can bind to proteins in a similar manner as ATP but is no longer hydrolyzed. Predict what would happen to helicase activity if AMP-PNP were added to a DNA replication reaction. Choose one: A. Helicase would function normally, since AMP-PNP is not the same as ATP and would not bind to helicase. B. Helicase would function faster than normal, since the AMP-PNP is not hydrolyzed. ATP binding induces conformational changes, but hydrolysis slows DNA unwinding by helicase. C. Helicase would no longer function, since the AMP-PNP is not hydrolyzed. ATP binding and hydrolysis induce the conformational changes that facilitate DNA unwinding by helicase. D. Helicase would function normally, since AMP-PNP is an analog of ATP and would function in the place of ATP.
C. Helicase would no longer function, since the AMP-PNP is not hydrolyzed. ATP binding and hydrolysis induce the conformational changes that facilitate DNA unwinding by helicase. Correct. ATP binding and hydrolysis are necessary for helicase function. AMP-PNP is not hydrolyzed like ATP, so it will block helicase conformational changes and function.
How are the primers from which DNA synthesis starts different from the DNA itself? Choose one: A. The primers have three phosphates on each nucleotide. B. The primers are not properly based paired so they can be removed. C. The primers are made up of RNA not DNA. D. The primers do not have a 3' -OH.
C. The primers are made up of RNA not DNA. RNA primers are made by an enzyme called primase to provide a "seed" from which the DNA polymer can grow. The primer provides a base paired 3'-OH for starting the reaction.
When DNA replication proceeds along a template, which of the following best describes the directionality of synthesis? Choose one: A. from telomere to telomere B. from the centromere to the telomeres C. in the 5'-to-3' direction D. in the 3'-to-5' direction E. in both the 3'-to-5' and the 5'-to-3' directions
C. in the 5'-to-3' direction Correct. DNA synthesis proceeds in the 5'-to-3' direction, meaning that nucleotides are added to the 3' end of a growing DNA strand.
Which term best describes DNA replication? Choose one: A. homologous B. conservative C. semiconservative D. dispersive
C. semiconservative Correct. In semiconservative replication, each DNA strand serves as a template.
What is the name of the protein that binds the two separated DNA strands to keep them from base pairing again before they can be replicated? Choose one: A. primase B. helicase C. single-strand binding protein D. sliding clamp
C. single-strand binding protein As a replication fork travels along the chromosome, the helicase pries apart the two strands of the double-helix. Single-strand binding protein holds these two strands apart and keeps them from reforming base pairs by binding to the single-stranded DNA.
A single DNA strand can serve as a template for both leading and lagging DNA strands during the synthesis of double-stranded DNA. Is this statement true or false? Choose one: A. true, but only for eukaryotic DNA replication B. true, but only for prokaryotic DNA replication C. true for all types of DNA replication D. completely false regardless of DNA type
C. true for all types of DNA replication
Which of the following is true about "junk DNA"? Choose one: A. It is found at the ends of chromosomes from over replication during each cell cycle. B. It usually codes for proteins but the proteins are nonfunctional in the cell. C. It serves no biological function and is all just a remnant from evolution. D. Portions of junk sequence are conserved between species and thus may be functional.
D. Portions of junk sequence are conserved between species and thus may be functional. Junk DNA is just a name given to portions of DNA for which the function is currently unknown. Some of these sequences have sequence similarity between species, suggesting they are conserved through evolution and thus may have function.
What is the first step that must occur to repair damage on one strand of the double helix? Choose one: A. The gap caused by the damage must be filled. B. The DNA backbone on both strands must be cut to make a double-strand break. C. The DNA backbone must be sealed. D. The damaged region must be removed.
D. The damaged region must be removed. Repair of damaged bases occurs through three steps. The first step is to remove the damaged base and the neighboring bases. Then, the gap can be filled using the undamaged strand as a template and the backbone sealed by ligase.
Meselson and Stahl performed a classic experiment to explore three models for the mechanism of DNA replication. Which of the models held that the two parental strands would remain associated after replication? Choose one: A. dispersive B. semiconservative C. liberal D. conservative
D. conservative The conservative model of replication posited that after replication of the parental strands, the original parental molecule remained intact. In this model, the two newly replicated strands would associate, forming their own new molecule.
What types of bonds are formed between histone proteins and DNA to form nucleosome core particles? Choose one: A. phosphodiester bonds B. polar covalent bonds C. nonpolar covalent bonds D. electrostatic interactions
D. electrostatic interactions Histone proteins are highly positively charged due to their composition from a large number of basic amino acids. This allows them to interact with the negatively charged DNA backbone.
In which direction, and on which strands does DNA replication proceed from a replication origin on a chromosome? Choose one: A. from the left to the right, on both strands B. only on one strand in the 5' → 3' direction C. only on one strand in the 3' → 5' direction D. in both directions, on both strands
D. in both directions, on both strands The DNA replication machinery can only add nucleotides in the 5' to 3' direction, but both strands are replicated using a clever workaround by the cell. In addition, replication forks move in both directions from a replication origin.
What type of enzyme removes damaged DNA from the rest of the DNA molecule? Choose one: A. polymerase B. helicase C. primase D. nuclease E. ligase
D. nuclease During DNA repair, nuclease breaks the phosphodiester bonds that hold the damaged or incorrect nucleotide in the DNA strand (Step 1 in the figure below). Once removed, a repair polymerase replaces the damaged nucleotide, using the other strand as the template to insert the proper nucleotide (Step 2), and then ligase seals the remaining nick by forming the remaining phosphodiester bond (Step 3).
What type of enzyme fills in the gap after damaged DNA has been removed? Choose one: A. nuclease B. ligase C. helicase D. polymerase E. primase
D. polymerase Correct. Specifically, a "repair polymerase" fills in this gap. DNA polymerase is involved in the reaction of 5'-to-3' addition of new DNA nucleotides to a polymer. A "repair polymerase" fills in the gap after damaged DNA has been removed. This enzyme is very similar to the DNA polymerase that catalyzes the reaction of 5'-to-3' addition of new DNA nucleotides to a growing DNA strand. Additionally, it has the same type of proofreading activity to ensure that the nucleotide that has been inserted to replace the error is, indeed, the correct one.
What is the name of the DNA sequence where replication begins? Choose one: A. replication fork B. DNA template C. initiator D. replication origin
D. replication origin DNA synthesis begins at replication origins, where local strand separation is promoted by initiator proteins.
Consider the image of two Okazaki fragments becoming covalently linked together and then answer the question. The enzyme that catalyzes the reaction depicted in the image is a DNA.
DNA Ligase Correct. DNA ligase joins together Okazaki fragments on the lagging strand during DNA synthesis.
The production of a continuous new strand of DNA using the many separate Okazaki fragments (in other words, the joining of the already made fragments) found on the lagging strand requires all of the following except which one? Choose one: repair polymerase DNA primase ATP DNA ligase nuclease
DNA primase Correct. Primase is needed to place the RNA primer required to initiate DNA synthesis. The joining of Okazaki fragments occurs at a later time.
Consider the process that a cell uses to replicate its double-stranded DNA before undergoing cell division. Which statement describes the DNA in the resulting daughter cells? Choose one: A. Each daughter cell receives a random mix of parental chromosomes and new chromosomes. B. Each strand of DNA in the daughter cells contains a mix of both newly replicated and parental DNA. C. The daughter cells receive only newly synthesized DNA; the parent cell keeps the original DNA. D. The double helix in one daughter cell consists of two strands that were originally in the parent cell, while the double helix in the other daughter cell consists of two newly made strands. E. The double helix in each daughter cell consists of one parental strand and one newly synthesized strand.
E. The double helix in each daughter cell consists of one parental strand and one newly synthesized strand. Correct. Based on the process that a cell uses to replicate its double-stranded DNA before undergoing cell division, the double helix in each daughter cell consists of one parental strand and one newly synthesized strand.
Which of the following describes a primer used in DNA replication? Choose one: A. a short segment of DNA, about 10 nucleotides in length B. a short segment of DNA, about 100 nucleotides in length C. a short segment of RNA, about 100 nucleotides in length D. a short segment of RNA that serves as a template for synthesizing an Okazaki fragment E. a short segment of RNA, about 10 nucleotides in length
E. a short segment of RNA, about 10 nucleotides in length Correct. The primers used during DNA replication are only about 10 nucleotides in length and are made of RNA. These RNA segments are synthesized by an enzyme called primase.
When compared to each other, the two replication forks that form at an origin of replication move in which direction? Choose one: A. in the 5'-to-3' direction B. in the 3'-to-5' direction C. toward the template strand D. toward the origin E. in opposite directions
E. in opposite directions Correct. The two forks move away from the origin in opposite directions. As DNA replication continues, these forks move farther and farther apart.
What does depurination refer to?Choose one: A. the loss of thymine due to damage from UV radiation B. the breaking of the DNA backbone C. the accumulation of mutations and subsequent loss of purity of a nucleotide sequence D. the loss of G or C bases from DNA E. the loss of A or G bases from DNA
E. the loss of A or G bases from DNA Correct. Depurination removes a purine base, leaving a gap in the DNA. Both adenine and guanine are purine bases.
Determine whether the following statement is true or false: During DNA replication, DNA polymerase initiates a completely new DNA strand from scratch.
False Correct. During DNA replication, DNA polymerase cannot initiate a completely new DNA strand from scratch. A short piece of RNA, called a primer, provides a starting point for DNA polymerase.
Determine whether the following statement is true or false: When a cell divides, its chromatin structure is completely reset?
False Correct. This form of "cell memory" is an important feature in how multicellular organisms are able to maintain specific tissue types as the organism grows and differentiates.
Determine whether the following statement is true or false: If an origin of replication is removed from a eukaryotic chromosome, the DNA on either side will also be lost, as it cannot be replicated.
False If one replication origin is removed, the DNA that would normally be replicated from that origin will instead be replicated from a neighboring origin. The process of DNA synthesis is begun by initiator proteins that bind to specific DNA sequences called replication origins. Here, the initiator proteins pry the two DNA strands apart, breaking the hydrogen bonds between the bases.
Determine whether the following statement is true or false: Histone tail modifications establish and maintain the different chromatin structures found in heterochromatin and euchromatin.
True The tails of all four of the core histones are particularly subject to covalent modifications, which include the addition (and removal) of acetyl, phosphate, or methyl groups. Can this happen in both euchromatin and heterochromatin? How does chromatin remodeling relate to this?
At a replication fork, how is the leading strand synthesized?Choose one: continuously without the use of a template in the incorrect 5'-to-3' direction in the correct 3'-to-5' direction discontinuously
continuously At a replication fork, the leading strand is synthesized continuously. A sliding clamp protein allows the DNA polymerase to move along the leading-strand template without falling off. In constrast, the lagging strand is synthesized discontinuously with multiple Okazaki fragments that need to be ligated together. All DNA synthesis involves a template strand and occurs in the correct 5'-to-3' direction as nucleic acids cannot be synthesized in the 3'-to-5' direction. Polymerization of the leading strand occurs in the correct 5'-to-3' direction.
At a replication fork, how is the lagging strand synthesized? Choose one: in the incorrect 3'-to-5' direction without the use of a template continuously discontinuously in the correct 3'-to-5' direction
discontinuously Correct. At a replication fork, the lagging strand is synthesized discontinuously. The Okazaki fragments are then joined together to form a continuous new DNA strand.
The bonds that link two DNA strands together are Choose one: phosphodiester bonds. hydrogen bonds. phosphoanhydride bonds. electrostatic interactions.
hydrogen bonds. Two DNA strands are held together by many weak noncovalent hydrogen bonds between complementary base pairs.
The energy for DNA polymerization is provided by the hydrolysis of which of the following? Choose one: pyrophosphate (releasing Pi) GTP (releasing Pi) incoming nucleoside triphosphates (releasing PPi) ATP (releasing Pi) the 3' end of the growing strand (releasing H2O)
incoming nucleoside triphosphates (releasing PPi) Correct. Hydrolysis of a high-energy phosphate bond in an incoming nucleotide, with the release of PPi, fuels DNA polymerization.
Which of the following best defines a mutation? Choose one: harmful change in a DNA sequence permanent change in a DNA sequence mistake created by faulty mismatch repair by-product of natural selection change in DNA sequence that causes a change in an amino acid in a protein
permanent change in a DNA sequence Correct. A mutation is a permanent change in a DNA sequence. Mutations can arise during DNA replication, and if the event is not repaired, then the genetic change will be inherited by the daughter cells.
The energy for the polymerization reaction in DNA synthesis is powered by Choose one: the association/disassociation cycles of the DNA polymerase enzyme. the formation of the phosphodiester bonds between nucleotides. the breaking of the hydrogen bonds between complementary base pairs. the breaking of high-energy phosphate bonds in the deoxynucleotides.
the breaking of high-energy phosphate bonds in the deoxynucleotides. Formation of the phosphodiester bonds requires input of energy. This is provided by the hydrolysis of the high-energy phosphoanhydride bonds in the incoming nucleotide triphosphates that are the building blocks for the DNA polymer.
