DNA Replication and DNA Storage Practice Test

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• What must first happen to DNA before it can be replicated?
• What is the structure formed when DNA is coiled around bundles of eight to nine histone proteins?
• In which cell cycle phase does origin licensing occur in eukaryotes?
• How is replication fidelity maintained during DNA synthesis?
• 3' → 5' exonuclease function allows polymerases to perform what action?
• Which DNA replication enzyme has a 5' → 3' exonuclease function to remove the primer?
• Which RNA is globular?
• How do Reed-Solomon codes assist in error correction for DNA data storage?
• From which location on a DNA strand do exonucleases remove nucleotides?
• What term describes the starting point where DNA replication begins?
• What function does DNA polymerase alpha-primase perform in initiating DNA synthesis?
• Which DNA replication enzyme unzips DNA to form replication fork?
• What does telomerase do to extend the template strand?
• A complex transposon will code for which extra features?
• RNA primers on each Okazaki fragment are replaced with DNA by which enzyme?
• What nucleic acid group does telomerase possess that allows it to bind to the flanking 3' end of the telomere?
• What problem at chromosome ends arises during replication, and which enzyme counteracts it?
• Which helicase complex unwinds DNA at replication forks in eukaryotes?
• Which repair pathway fixes oxidative and deaminated bases and abasic sites?
• After replication in prokaryotes, the strand that has just been synthesized is typically:
• How is replication timing coordinated with the S phase in eukaryotes?
• What storage conditions optimize DNA longevity for archival purposes?
• Compare direct binary-to-DNA mapping with encoding schemes that use an intermediate symbol set.
• Which DNA replication enzyme 'glues' two strands of DNA together?
• What is the role of primase in replication?
• What is the direction of the new antiparallel strand synthesized by DNA polymerase?
• Which chromatin is loosely bound to nucleosomes and actively transcribed?
• Which enzyme is primarily responsible for removing RNA primers on the lagging strand in bacteria?
• In eukaryotes, which polymerases synthesize the leading and lagging strands, and what role does Pol alpha-primase play?
• Which term describes proteins that stabilize the unwound single strands during replication?
• Which RNA transports amino acids to the ribosome?
• Which statement best describes prokaryotic origins of replication?
• What is a major challenge associated with PCR amplification in DNA data storage?
• Which DNA replication enzyme creates a small strip of RNA where DNA polymerase takes over to add DNA nucleotides?
• Satellite DNA is concentrated at centromeres and ends of chromosomes.
• Telomeres consist of repetitive sequences at chromosome ends to protect the DNA. Which statement is true about telomeres?
• Which plasmid replication mechanism is characterized by unidirectional replication around the circle, often generating a single-stranded DNA intermediate?
• Which statement describes replication initiation in bacteria such as Escherichia coli?
• What are address blocks and how do they support random access in DNA storage?
• In eukaryotes, what is the function of the Origin Recognition Complex (ORC)?
• What are the two types of chromatin that exist during interphase?
• RNA primers during prokaryotic replication are removed by which mechanism?
• What does random access rely on?
• Which enzyme relieves supercoiling ahead of the replication fork?
• Which DNA replication enzyme synthesizes the new strand of DNA?
• Which domain of organisms uses multiple origins of replication?
• What process begins at origins of replication in the middle of a DNA molecule?
• Which DNA replication enzyme keeps DNA strands separate?
• How do prokaryotic origins differ from eukaryotic origins?
• What is DNA data storage and why is it considered high-density storage?
• Which enzymes relieve torsional stress ahead of the replication fork?
• What is the typical data payload per DNA oligo used in demonstrations, including adapters?
• Which function is not typically performed by the leading-strand replication proteins?
• Which repair mechanism removes bulky lesions and UV-induced thymine dimers?
• Which process fills gaps left after RNA primers are removed during replication?
• What is the result if transposons are inserted into another region?
• In bacteria, which protein complex recognizes and initiates repair in MMR?
• What is the purpose of error-correcting codes in DNA-based data storage?
• Which statement best describes the proofreading capability of DNA polymerases in prokaryotes?
• A simple transposon consists of an insertion sequence that contains 1 gene that codes for what structure?
• The leading strand is synthesized in which direction relative to the replication fork?
• Which of the following describes origin licensing in eukaryotes?
• Which enzyme is part of the replication machinery and resolves torsion by cutting a strand?
• What are DNA segments that can move to a new location on either the same or different chromosome?
• During replication, the strand synthesized in short fragments on the lagging strand is called
• Which polymerase purely functions in replication?
• Which strand is synthesized as Okazaki fragments during lagging-strand synthesis?
• What type of replication is DNA replication?
• What is the effect on the genome when transposons insert into a gene region?
• Which factor stabilizes the unwound single strands during replication?
• Which chromatin contains a large amount of satellite DNA?
• How does chromosomal replication differ from plasmid replication in bacteria?
• How do error-correcting codes impact data integrity in DNA storage?
• Which enzyme relieves torsional stress ahead of the replication fork?
• How does telomerase extend chromosome ends without a conventional template at the edge?
• What is the role of topoisomerases during replication?
• In prokaryotes, how is the strand without any errors modified after it has been successfully replicated?
• Which step directly follows DNA synthesis in the workflow?
• Telomerase activity is most pronounced in which cells?
• Which enzyme unzips the double helix to form the replication fork?
• Approximately how many genes are present in the human genome?
• What is the typical length range for DNA oligos used in experimental DNA data storage demonstrations?
• Which proteins load the MCM2-7 helicase onto DNA during eukaryotic origin licensing?
• Which base is used in RNA instead of thymine?
• Which enzyme is primarily responsible for adding nucleotides to a growing DNA strand?
• What is the enzyme that attaches to the end of the template strand and extends the template strand?
• Former genes that have accumulated mutations over a long time and no longer produce a functional protein are called
• Which DNA replication enzyme has some proofreading function?
• Which DNA strand is synthesized discontinuously?
• What types of errors dominate in DNA synthesis and sequencing for data storage?
• Which chromatin type contains a large amount of satellite DNA?
• Why is avoiding long homopolymers important in DNA data storage?
• Which chromatin type is generally more transcriptionally inactive and densely packed?
• Which polymerases possess a 3' to 5' exonuclease proofreading activity?
• Which pattern characterizes the lagging strand?
• When DNA strands separate, what space forms that expands in both directions?
• During which cellular stage is a second chromatid containing a copy of DNA assembled?
• Which statement best describes how origin licensing prevents re-initiation in the same cell cycle in eukaryotes?
• Telomere maintenance by telomerase is particularly important in which cell types?
• Which enzyme is primarily responsible for relieving torsional stress by cutting and rejoining DNA strands?
• What are the components and primary activity of telomerase?
• Which chromatin contains areas of tightly packed nucleosomes and appears darker?
• In replication, the leading strand is synthesized in which direction?
• What is the function of RNA primers in replication, and what happens after their job is done?
• Which repair pathway detects and corrects small insertions, deletions, and base mispairs?
• During which specific phase of interphase is DNA replicated?
• Which statement best describes the composition of each newly formed DNA molecule after replication?
• Which protein stabilizes the single-stranded DNA after unwinding?
• Which DNA replication enzymes have a 3' → 5' exonuclease function?
• Which pattern of synthesis characterizes the leading strand?
• What are the short DNA fragments synthesized on the lagging strand called?
• Which activity provides proofreading during DNA synthesis?
• Which feature has major and minor grooves in the double helix?
• Which enzyme seals the sugar-phosphate backbone after replication?
• During DNA replication, the leading strand is best described as which of the following?
• During the replication process, which phase is responsible for copying the DNA?
• DNA primase creates what starting point for DNA synthesis?
• What are fragments produced by DNA polymerase on the lagging strand?
• Which protein prevents the separated DNA strands from re-annealing during replication?
• In which direction can DNA polymerase I proofread while laying down a new nucleotide strand?
• Which statement about DNA polymerase I is true?
• In bacterial replication initiation, which statement describes how the DnaB helicase is loaded onto DNA after origin melting?
• Which action best describes the general outcome of mismatch repair after replication?
• In which direction does DNA polymerase I primarily break down the RNA primer via exonuclease function?
• Which enzyme seals nicks between Okazaki fragments on the lagging strand?
• Why do prokaryotes not have an issue with telomere shortening?
• What is the function of the sliding clamp PCNA in DNA replication?
• Which DNA strand is synthesized continuously?
• Which polymerase synthesizes the leading strand in eukaryotes?
• How does the speed of replication in prokaryotes compare to the speed of replication in eukaryotes?
• Which statement correctly describes the synthesis of the leading strand during DNA replication?
• Which statement about PCNA is true?
• Which domain of organisms uses one origin of replication?
• DNA ligase seals nicks to join fragments.
• How can random access be achieved in a DNA data storage system?
• Which enzyme unwinds the DNA double helix ahead of the replication fork?
• Before DNA base pairs can be added to a new strand what addition is required?
• Name two error-correcting approaches used in DNA data storage.
• The DNA that remains largely noncoding and repetitive constitutes the majority of the genome.
• Which DNA replication enzyme functions in DNA repair?
• In bacterial replication initiation, which protein is primarily responsible for starting the process at the origin?
• What constraints must be considered when encoding data into DNA sequences?
• Which statement about repetitive DNA is true?
• Which checkpoint pathways monitor replication fork integrity and coordinate cell cycle progression?
• What type of DNA makes up most of the genome and does not code for proteins or RNA?
• Which DNA polymerase purely functions in replication?
• Which RNA is clover-shaped?
• Compare direct binary-to-DNA mapping with encoding schemes that use an intermediate symbol set.
• Which statement describes pseudogenes?
• How does GC content affect DNA storage stability and readability?
• What provides energy for DNA elongation?
• Which enzyme relieves torsional strain during replication?
• What is the role of RFC in DNA replication?
• What is the basic unit of chromatin formed by DNA wrapped around histones?
• Which RNA is linear?
• In which domain of organisms are DNA polymerases I, II and III present?
• Outline a high-level pipeline for DNA data storage from data to retrieval.
• Because DNA polymerase cannot extend DNA after removing the RNA primer, what happens to the telomeres with each replication cycle?
• Which enzyme connects Okazaki fragments?
• Which enzyme catalyzes the synthesis of a new DNA strand by adding nucleotides?
• Which enzyme adds nucleotides to a growing DNA strand and works in the 5' to 3' direction?
• Which enzyme is primarily responsible for unwinding the DNA at the fork on the leading strand?
• What is a key difference in origin activation between prokaryotes and eukaryotes?
• In bacteria, which factors initiate replication at the origin and which region is melted to permit loading of the helicase?
• What is the function of telomerase in chromosome maintenance?
• How is data density defined in DNA storage and what limits it?
• Which DNA repair pathway corrects base-base mismatches after replication?
• What is the theoretical maximum data density per base?
• In DNA replication, which enzyme seals the sugar-phosphate backbone once replication is complete?
• Which checkpoint pathway primarily responds to double-strand breaks in DNA?
• Which molecule has functional roles in the cell and varies by type?
• Which structure consists of 5' to 3' phosphodiester bonds to form a sugar-phosphate backbone?
• How is replication prevented from re-initiating origins within the same cell cycle in eukaryotes?
• Which part of the strand still needs to be replicated after the information-carrying DNA is replicated?
• Which term best describes the strand that is synthesized continuously toward the replication fork?
• What are large tandem repeats of noncoding DNA concentrated at centromeres and ends of chromosomes?
• Which enzyme carries out primer removal in prokaryotic DNA replication via 5' to 3' exonuclease activity?
• What regulates origin licensing and firing in eukaryotic S-phase?
• What is the function of telomeres?
• What are telomeres and why are they important for genome stability?
• Okazaki fragments are produced on which strand?
• In the absence of telomerase activity, telomeres in most somatic cells tend to do what during successive divisions?
• Which statement best describes the impact of GC content on sequencing and synthesis in DNA data storage?
• Which DNA replication enzyme eases the tension of coiled DNA by introducing nicks and cuts into the DNA strand?
• Which RNA forms the structural and catalytic core of ribosomes?
• What ensures that the overall data integrity in DNA storage can be recovered even if some sequences are missing or severely damaged?
• Which statement best describes the end-replication problem?
• Which RNA carries genetic information from DNA to the ribosome to specify amino acid sequence?
• Which polymerase synthesizes the lagging strand in eukaryotes?
• Which enzyme is responsible for unwinding the double helix at the replication fork on the leading strand?
• What is the role of DNA polymerase I in bacteria during replication?
• Which enzyme creates an RNA primer to initiate DNA synthesis?
• What problem arises when there is not enough template strand at the end of a telomere?
• What role does sequencing play in retrieving data from DNA storage?
• In DNA replication, which direction does the DNA polymerase move along the template strand?