Question 1

Topoisomerases – Which statement about E. coli DNA gyrase is accurate?

Accepted Answer

Introduction: DNA gyrase is a type II topoisomerase unique to bacteria that introduces negative supercoils into DNA, which is crucial for replication, transcription, and chromosome compaction. This question examines core functional and pharmacological properties of gyrase. Given Data / Assumptions: Gyrase modulates DNA supercoiling state. Bacterial topoisomerases are targets of antibiotics (e.g., quinolones, fluoroquinolones). DNA transactions throughout the chromosome require supercoil management. Concept / Approach: Gyrase introduces negative supercoils and removes positive supercoils ahead of replication forks and transcription complexes. Fluoroquinolone antibiotics (e.g., ciprofloxacin) inhibit gyrase by stabilizing DNA–enzyme cleavage complexes, blocking religation and leading to lethal double-strand breaks. Gyrase is required globally, not just at oriC, and it is not a helicase (which unwinds duplex DNA by strand separation). Step-by-Step Solution: Recall gyrase activity: introduces negative supercoils using ATP.Note pharmacology: quinolones bind gyrase–DNA complexes, preventing religation.Recognize cellular roles: replication, transcription, and chromosome maintenance.Eliminate statements that misassign function or localization. Verification / Alternative check: Genetic and biochemical assays demonstrate accumulation of positive supercoils and growth arrest upon gyrase inhibition; quinolone resistance mutations map to gyrA/gyrB genes, confirming drug target identity. Why Other Options Are Wrong: Adds positive supercoils: opposite of normal gyrase role. Only at oriC: gyrase acts genome-wide. Same as helicase: different enzymes; helicase separates strands, gyrase alters topology. Exclusively in transcription: it functions in multiple DNA processes. Common Pitfalls: Conflating supercoiling management (topoisomerases) with strand unwinding (helicases) or assuming gyrase is restricted to initiation sites. Final Answer: It can be inhibited by specific antibiotics (e.g., quinolones).

Question 2

DNA replication fidelity – Which enzyme is directly responsible for proofreading base pairing during DNA synthesis?

Accepted Answer

Introduction: High-fidelity DNA replication depends on accurate base selection and post-incorporation error correction. The central proofreading step is carried out by the replicative DNA polymerases through exonuclease activity. This question asks you to identify the enzyme that performs proofreading directly at the replication fork. Given Data / Assumptions: Replicative polymerases possess 3'→5' exonuclease activity for proofreading. Accessory enzymes have distinct functions (e.g., ligation, primer synthesis, end maintenance). Proofreading corrects mispaired nucleotides immediately after insertion. Concept / Approach: DNA polymerases (e.g., bacterial Pol III; eukaryotic Pol δ and Pol ε) monitor the geometry of nascent base pairs. Upon detecting a mismatch, the polymerase shifts the primer terminus to a 3'→5' exonuclease site, excises the incorrect nucleotide, and then resumes synthesis. This intrinsic activity greatly lowers the error rate before mismatch repair pathways act. Step-by-Step Solution: Synthesis proceeds with correct Watson–Crick pairing.If a mismatch occurs, the polymerase stalls due to poor fit.The 3' end is transferred to the exonuclease site.Incorrect nucleotide is removed; polymerase repositions to the polymerase site.Synthesis resumes with the correct nucleotide. Verification / Alternative check: Mutations disabling polymerase exonuclease increase mutation rates dramatically, demonstrating the essential role of polymerase-based proofreading in genomic fidelity. Why Other Options Are Wrong: Telomerase: extends telomeres; does not proofread replication errors. Primase: synthesizes RNA primers; lacks proofreading. DNA ligase: seals nicks; does not check base pairing. Topoisomerase I: manages supercoils; unrelated to base selection. Common Pitfalls: Attributing proofreading to mismatch repair (a separate, downstream pathway) rather than to polymerase exonuclease activity at the fork. Final Answer: DNA polymerase

Question 3

Enzymology – The Klenow fragment of E. coli DNA polymerase I, in the absence of free dNTPs, shows which activity?

Accepted Answer

Introduction: The Klenow fragment is a large proteolytic fragment of E. coli DNA polymerase I that retains the polymerase and 3'→5' exonuclease domains but lacks the 5'→3' exonuclease domain. Understanding its retained activities is essential for its use in cloning, labeling, and blunt-end polishing. Given Data / Assumptions: Klenow fragment lacks 5'→3' exonuclease activity. It still contains polymerase and 3'→5' exonuclease (proofreading) functions. Polymerase activity requires free dNTPs; exonuclease activity does not. Concept / Approach: Without available dNTP substrates, Klenow cannot extend DNA strands, but it can still remove mismatched or terminal nucleotides via its proofreading exonuclease. This property allows limited trimming or quality control of DNA ends even when synthesis cannot proceed. Step-by-Step Solution: Recognize domain composition of Klenow: polymerase + 3'→5' exonuclease.Remove dNTPs from the reaction: polymerase activity is halted.Remaining function: 3'→5' exonuclease can excise nucleotides from the 3' end.Conclusion: Klenow exhibits exonuclease activity without free nucleotides. Verification / Alternative check: Biochemical assays show degradation of mismatched 3' termini by Klenow in nucleotide-free conditions, demonstrating persistent proofreading capability independent of synthesis. Why Other Options Are Wrong: Endonuclease/nickase/helicase: activities not present in Klenow. No activity: incorrect; exonuclease remains active. Common Pitfalls: Confusing 5'→3' exonuclease (absent in Klenow) with 3'→5' proofreading (retained), or assuming all polymerase-associated activities require dNTPs. Final Answer: Exonuclease activity (3'→5' proofreading)

Question 4

Nucleic acid basics – In double-stranded DNA, guanine (G) base-pairs with which base?

Accepted Answer

Introduction: Correct base pairing in DNA ensures accurate replication and transcription. Recognizing the standard Watson–Crick partners is a foundational competency in genetics and molecular biology courses. Given Data / Assumptions: DNA uses the bases A, T, G, and C. Base pairing relies on specific hydrogen bonding patterns. Uracil replaces thymine only in RNA. Concept / Approach: Guanine pairs with cytosine via three hydrogen bonds in canonical B-DNA, contributing to the higher thermal stability of GC-rich sequences compared with AT-rich sequences. This stability is reflected in higher melting temperatures for GC-rich duplexes and is exploited in PCR primer design and genome analysis. Step-by-Step Solution: List canonical pairs: A–T and G–C.Exclude RNA-specific bases (U) from DNA pairing.Select cytosine as the correct partner for guanine.Acknowledge the stronger bonding (three H-bonds) relative to A–T (two H-bonds). Verification / Alternative check: Empirical nearest-neighbor thermodynamics show increased duplex stability with GC content, confirming the stronger pairing of G–C relative to A–T pairs. Why Other Options Are Wrong: Adenine/thymine: pair with each other, not with guanine. Uracil: present in RNA, not DNA. Hypoxanthine: appears in certain wobble or deamination contexts, not standard DNA pairing. Common Pitfalls: Mixing RNA and DNA base-pair rules or assuming identical stability for all pairs. Final Answer: Cytosine (C)

Question 5

DNA replication models – Which hypothesis correctly describes how DNA replicates in cells?

Accepted Answer

Introduction: The mechanism of DNA replication was a central question resolved by the Meselson–Stahl experiment. Understanding the difference between conservative, semi-conservative, and dispersive models is essential for interpreting replication intermediates and isotope-labeling outcomes. Given Data / Assumptions: Each DNA duplex contains two antiparallel strands. Replication requires templated synthesis. Isotopic labeling can distinguish old from newly synthesized DNA based on density. Concept / Approach: In semi-conservative replication, each daughter duplex contains one parental (old) strand and one newly synthesized strand. After one round of replication in 14N medium following 15N labeling, all DNA becomes hybrid density; after the second round, two bands (hybrid and light) appear—patterns inconsistent with purely conservative or purely dispersive models. Step-by-Step Solution: Define models: conservative (old duplex retained intact), semi-conservative (strand splitting), dispersive (patchwork).Predict densities for each model after replication in 14N media.Compare predictions with experimentally observed banding in CsCl gradients.Only semi-conservative predictions match the data. Verification / Alternative check: Pulse–chase experiments and visualization of replication forks also corroborate strand-separation mechanisms consistent with semi-conservative copying. Why Other Options Are Wrong: Conservative: predicts distinct heavy and light bands after one round, not observed. Dispersive: predicts a single intermediate band that shifts each generation, not observed. Evolutionary or hybrid theories: not accepted replication mechanisms. Common Pitfalls: Confusing band patterns after first versus second replication cycles; semi-conservative yields hybrid after one, hybrid + light after two. Final Answer: Semi-conservative replication theory

Question 6

Bacterial genetics – What is the approximate size of the Escherichia coli genome expressed in kilobases (kb)?

Accepted Answer

Introduction: Genome size provides context for gene number, regulatory complexity, and replication timing. E. coli K-12 is a benchmark organism in microbiology and molecular genetics, and its genome size is widely cited in textbooks and databases. Given Data / Assumptions: Genome size is commonly reported in base pairs or kilobases/megabases. E. coli K-12 laboratory strains have well-characterized genomes. Approximation within a few percent is acceptable in survey questions. Concept / Approach: The E. coli K-12 genome is approximately 4.6 megabases (Mb), which equals about 4600 kilobases (kb). Among the choices, 4500 kb is the closest reasonable approximation. Natural isolates may vary slightly, but ~4.5–4.7 Mb is a robust rule of thumb for teaching purposes. Step-by-Step Solution: Recall benchmark: E. coli genome ≈ 4.6 Mb.Convert Mb to kb: 4.6 Mb ≈ 4600 kb.Compare with options: 4500 kb is nearest to 4600 kb.Select 4500 kilobase as the approximate size. Verification / Alternative check: Reference genome assemblies report sizes near 4.6 Mb for K-12 MG1655, supporting the 4500–4600 kb approximation used in educational contexts. Why Other Options Are Wrong: 3000/1500 kb: far too small for E. coli. 5500/6500 kb: larger than commonly reported laboratory strains. Common Pitfalls: Confusing kilobases (kb) with kilobytes (kB) or megabases (Mb), and forgetting that 1 Mb = 1000 kb in genomics shorthand. Final Answer: 4500 kilobase

Question 7

General biology – Which of the following would not contain DNA?

Accepted Answer

Introduction: Deoxyribonucleic acid (DNA) is the hereditary material in almost all living organisms and many viruses (some viruses use RNA). Recognizing which entities possess DNA helps delineate the boundary between living systems and inanimate matter in biological contexts. Given Data / Assumptions: Cells (prokaryotic and eukaryotic) contain DNA. Fungi (yeast, molds) are eukaryotes with chromosomal DNA. Inanimate minerals or manufactured crystalline solids do not contain DNA unless contaminated. Concept / Approach: All cellular life, including bacteria, yeast, molds, plants, and animals, encodes genetic information in DNA. By contrast, glass crystals are nonliving, inorganic materials composed primarily of silicon dioxide networks without cellular structures or nucleic acids. Therefore, among the listed choices, glass crystals are the only item that inherently lacks DNA. Step-by-Step Solution: Identify living versus nonliving entries in the list.Confirm that bacteria, yeast, molds, and plant tissues are cellular and contain DNA.Recognize glass as an inorganic solid lacking cells and biomacromolecules.Select glass crystals as the entity without DNA. Verification / Alternative check: Microscopy and biochemical assays detect DNA in cells by staining (e.g., DAPI) or extraction methods; such approaches yield no DNA from clean, uncontaminated glass due to its nonbiological composition. Why Other Options Are Wrong: Yeast/mold: eukaryotic fungi with nuclear DNA. Bacteria: prokaryotes with circular chromosomes and often plasmids. Plant seeds: contain diploid plant embryos with DNA in nuclei, mitochondria, and plastids. Common Pitfalls: Assuming that acellular materials used in labs (e.g., agarose, glass) might contain DNA; they do not unless contaminated by biological samples. Final Answer: Glass crystals (inert nonliving material)

Question 8

Chromatin condensing in sperm heads  In animal reproduction and cell biology, DNA in mature sperm heads is extremely condensed. During spermiogenesis, canonical histones are largely replaced by which small, highly basic proteins that enable tight pa…

Accepted Answer

Introduction: Packaging the paternal genome inside a tiny sperm head requires an extraordinary level of compaction. This question tests knowledge of specialized chromatin proteins in spermiogenesis and how they differ from canonical histones used in somatic cells. Given Data / Assumptions: Mature sperm chromatin is far more condensed than mitotic chromosomes in somatic cells. Somatic nucleosomes use histones H2A, H2B, H3, and H4, with H1 as linker. Spermiogenesis features large scale chromatin remodeling with replacement of histones. Concept / Approach: The key concept is the replacement of histones by smaller, very basic proteins that neutralize DNA phosphate charges more efficiently. These proteins are rich in arginine and facilitate tight DNA supercoiling, yielding exceptional stability required for transit and fertilization. Step-by-Step Solution: 1) Identify the biological process: spermiogenesis leads to protamine rich chromatin.2) Recognize biochemical requirements: very basic proteins neutralize DNA and allow extreme compaction.3) Name the proteins: protamines, not purines or pyrimidines, which are nucleotide bases.4) Conclude that protamines replace most histones in mature sperm heads. Verification / Alternative check: Biochemical analyses show arginine rich protamines forming tight toroidal DNA loops. After fertilization, protamines are replaced by maternal histones, confirming their specialized and reversible role. Why Other Options Are Wrong: Purines and pyrimidines are nucleotide bases, not proteins. All of the above cannot be correct because only protamines fulfill the protein role required. Polyamines can assist DNA compaction but do not replace histones as the principal proteins in sperm chromatin. Common Pitfalls: Confusing small organic cations like spermidine with the protein based architecture of sperm chromatin. Another pitfall is assuming histones remain dominant in all cell types. Final Answer: Protamines

Question 9

UV radiation and DNA damage  In molecular genetics and cell biology, what is the principal damaging effect of ultraviolet radiation on DNA under physiological conditions?

Accepted Answer

Introduction: Ultraviolet radiation from sunlight can induce specific lesions in DNA that disrupt base pairing and replication. Recognizing the signature lesion of UV exposure is fundamental for understanding mutagenesis, DNA repair, and skin cancer biology. Given Data / Assumptions: Consider common solar UV wavelengths that reach the skin, mainly UVB with some UVA contribution. Assume hydrated DNA in a cellular environment with normal oxygen levels. Focus on the most frequent and characteristic lesion rather than rare secondary effects. Concept / Approach: UV photons are absorbed by adjacent pyrimidines in DNA, promoting a photochemical reaction that covalently links them. The dominant products are cyclobutane pyrimidine dimers, especially thymine dimers, and 6 4 photoproducts. These lesions distort the helix and block polymerases unless repaired. Step-by-Step Solution: 1) Identify UV target: adjacent pyrimidines on the same strand.2) Photochemistry links the C5 and C6 atoms to form a cyclobutane ring.3) Resulting thymine dimer prevents normal base pairing and stalls replication.4) Nucleotide excision repair removes the dimer, restoring DNA integrity when functioning properly. Verification / Alternative check: Epidemiology and genetics of xeroderma pigmentosum demonstrate the importance of repairing UV induced dimers. Failure to repair leads to high mutation rates and skin cancer susceptibility. Why Other Options Are Wrong: Depurination is a spontaneous hydrolytic event not specific to UV. Single strand breaks can occur but are not the hallmark UV lesion. Dehydration is not a DNA lesion. Oxidative 8 oxoG formation is more characteristic of ionizing radiation or reactive oxygen species. Common Pitfalls: Confusing UV damage with oxidative stress or ionizing radiation effects. Another pitfall is assuming all DNA damaging agents cause the same predominant lesion. Final Answer: Formation of thymine dimers

Question 10

Relative size comparison in nucleic acid components  Considering molecular structure, which of the following is the largest unit among these choices?

Accepted Answer

Introduction: Understanding the hierarchy of nucleic acid components helps with reasoning about DNA structure, synthesis, and biochemical assays. This question asks which listed entity is structurally largest as a discrete chemical unit. Given Data / Assumptions: A nucleotide is composed of a nitrogenous base, a pentose sugar, and one or more phosphates. A nitrogenous base alone is a single heterocyclic compound. A phosphate group is a small inorganic moiety. A carbon atom is a single element, not a molecular unit. Deoxyribose sugar is a component of a nucleotide but not as large as the full nucleotide. Concept / Approach: Compare composition. The nucleotide contains multiple components covalently linked and can carry one to three phosphates, making it the most massive unit among the options provided. All other choices are subunits or individual atoms that are incorporated into the nucleotide. Step-by-Step Solution: 1) List components: base + sugar + phosphate equals nucleotide.2) Recognize that each alternative is either a single component or smaller fragment.3) Conclude that the fully assembled nucleotide is the largest entity. Verification / Alternative check: Molecular weights illustrate the point. For example, dAMP has mass far exceeding either adenine alone or deoxyribose alone, and certainly larger than a phosphate group or an element such as carbon. Why Other Options Are Wrong: Nitrogenous base and deoxyribose represent partial components. Phosphate is a small group. A carbon atom is an element, not a macromolecular unit. Common Pitfalls: Confusing nucleoside with nucleotide. A nucleoside lacks phosphate and is smaller than a nucleotide, reinforcing that the nucleotide is largest among the listed units. Final Answer: Nucleotide

Question 11

DNA methylation patterns in eukaryotes  In eukaryotic genomes, what is the predominant and most common form of DNA methylation under normal physiological conditions?

Accepted Answer

Introduction: Epigenetic DNA methylation regulates gene expression, chromatin state, and genome stability. The most widespread and studied methyl mark in vertebrate eukaryotes occurs at specific cytosine contexts and is maintained through DNA replication by dedicated enzymes. Given Data / Assumptions: Focus on canonical DNA methylation in animals, particularly vertebrates. Exclude specialized or rare modifications that occur in certain species or developmental stages. Consider enzymatic pathways responsible for establishing and maintaining methylation patterns. Concept / Approach: DNA methyltransferases add a methyl group to carbon 5 of cytosine, primarily in CpG dinucleotides. This modification is symmetrical in double stranded DNA, enabling copying of the pattern after replication by maintenance methyltransferases. Step-by-Step Solution: 1) Identify the common substrate: cytosine in CpG context.2) DNMT enzymes write the mark during development and in somatic cells.3) Methyl CpG recruits proteins that compact chromatin and silence or modulate transcription.4) Patterns are heritable through cell division but dynamic during development and disease. Verification / Alternative check: Genome wide bisulfite sequencing maps demonstrate that the bulk of methylation resides at CpG sites in vertebrates, with islands, shores, and gene bodies showing context dependent patterns. Why Other Options Are Wrong: Adenosine or guanosine methylation is not the predominant canonical mark in vertebrate DNA. Thymine methylation is not the standard epigenetic mechanism in these organisms. None of the above cannot be correct because cytosine in CpG is well established. Common Pitfalls: Conflating RNA methylation with DNA methylation, or generalizing plant specific contexts to vertebrates. Another pitfall is mixing histone methylation with DNA methylation. Final Answer: Cytosine methylation in CpG dinucleotides

Question 12

Linker DNA and histone association in nucleosomes  Within chromatin architecture, which histone is primarily associated with linker DNA and helps stabilize higher order structure?

Accepted Answer

Introduction: Nucleosomes compact eukaryotic DNA by wrapping it around histone octamers. Beyond the core histones, an additional histone associates with linker DNA between nucleosomes and contributes to chromatin fiber organization and stability. Given Data / Assumptions: Core nucleosome contains two copies each of H2A, H2B, H3, and H4 with about 146 base pairs of wrapped DNA. Linker DNA connects adjacent nucleosomes and varies in length by cell type and species. A distinct histone binds at the dyad and engages linker DNA, promoting compaction. Concept / Approach: Histone H1, often called the linker histone, binds near the nucleosomal dyad and contacts linker DNA. This reduces DNA accessibility and promotes formation of higher order fibers, modulating gene regulation by changing chromatin openness. Step-by-Step Solution: 1) Identify core versus linker associated histones.2) Recognize H1 function at the entry and exit points of DNA on the nucleosome.3) Conclude H1 is the principal linker associated histone. Verification / Alternative check: Biophysical studies show that H1 binding compacts arrays into higher order structures. Knockdown experiments increase chromatin accessibility, validating this role. Why Other Options Are Wrong: H2A, H2B, H3, and H4 form the core octamer, not the linker binder. CENP A is a centromeric H3 variant specific for kinetochore chromatin, not general linker association. Common Pitfalls: Assuming all histones behave identically or confusing H1 with core histones. Another pitfall is equating histone variants with linker function without evidence. Final Answer: Histone H1

Question 13

Okazaki fragments and DNA synthesis  In DNA metabolism, Okazaki fragments are characteristic intermediates that arise during which process?

Accepted Answer

Introduction: DNA replication must copy antiparallel strands using polymerases that extend only in the 5 to 3 direction. This asymmetry forces one strand to be synthesized discontinuously as short DNA segments known as Okazaki fragments. Given Data / Assumptions: DNA polymerases synthesize DNA by adding nucleotides to a 3 hydroxyl end. Replication forks are bidirectional with leading and lagging strands. Okazaki fragments are later joined by ligase to create a continuous lagging strand. Concept / Approach: The leading strand can be synthesized continuously toward the fork. The lagging strand runs in the opposite direction relative to polymerase polarity, requiring repeated priming and extension away from the fork, generating many short fragments that are processed into a continuous strand. Step-by-Step Solution: 1) Identify polymerase directionality: extension occurs 5 to 3.2) Assign leading strand as continuous synthesis.3) Assign lagging strand as discontinuous synthesis producing Okazaki fragments.4) Use DNA ligase to seal nicks after primer removal and gap filling. Verification / Alternative check: Pulse labeling experiments and electron microscopy reveal short nascent DNA pieces on the lagging strand that mature into full length DNA after ligation. Why Other Options Are Wrong: Transformation is DNA uptake by cells. PCR uses continuous primer extension in vitro and does not generate classical lagging strand fragments. General protein synthesis and transcription do not involve DNA fragment ligation. Common Pitfalls: Assuming both strands are continuous or believing polymerases can extend 3 to 5. Another pitfall is confusing Okazaki fragments with RNA primers. Final Answer: Replication

Question 14

Methods for DNA sequencing  In classical molecular biology, which approaches can be used to determine the nucleotide sequence of DNA?

Accepted Answer

Introduction: Two foundational approaches established DNA sequencing as a routine laboratory procedure. Knowing their names and principles is essential context for modern high throughput methods that evolved from these techniques. Given Data / Assumptions: Chemical degradation refers to the Maxam Gilbert method. Chain termination refers to the Sanger method using dideoxynucleotides. Focus on historically validated approaches rather than speculative physical methods. Concept / Approach: The Maxam Gilbert approach uses base specific chemical cleavage followed by gel separation to read sequence. The Sanger approach uses polymerase driven synthesis that terminates at labeled dideoxynucleotides, allowing readout by size separation. Both accurately recover base order. Step-by-Step Solution: 1) Identify chemical degradation strategy producing fragments ending at specific bases.2) Identify chain termination strategy that halts synthesis at incorporated ddNTPs.3) Resolve fragment ladders by electrophoresis to deduce sequence.4) Confirm that both methods yield base by base information. Verification / Alternative check: Classical sequencing of phage and plasmids used these methods successfully for decades, later automated with fluorescent labels leading to capillary sequencing instruments. Why Other Options Are Wrong: Purely physical optical approaches without chemistry were not the standard historical methods. Random shearing without detection cannot produce a sequence readout. Common Pitfalls: Confusing chain termination with chain elongation only, or assuming chemical cleavage is obsolete and therefore incorrect. Both are valid methods even if one is now rarely used. Final Answer: Both chemical degradation and chain termination methods

Question 15

Directionality of DNA replication  During chromosomal DNA synthesis by DNA polymerases, nucleotide addition and strand elongation proceed in which direction?

Accepted Answer

Introduction: DNA polymerases have strict chemical polarity. Understanding this polarity explains the existence of leading and lagging strands, Okazaki fragments, and specific nuclease activities involved in replication fidelity and primer removal. Given Data / Assumptions: Nucleotides are added to a free 3 hydroxyl group on the growing strand. Incoming deoxynucleoside triphosphates provide the energy for bond formation. Replication forks manage antiparallel templates using leading and lagging strategies. Concept / Approach: The chemistry of phosphodiester bond formation requires nucleophilic attack by the 3 hydroxyl on the alpha phosphate of the incoming nucleotide. This enforces 5 to 3 strand growth regardless of species, although different polymerases participate. Step-by-Step Solution: 1) Define polymerase action: extend only from a 3 hydroxyl end.2) Conclude that elongation direction is 5 to 3 relative to the newly synthesized strand.3) Connect this to replication architecture, where one strand must be discontinuous.4) Recognize that proofreading often uses a separate 3 to 5 exonuclease, not reverse synthesis. Verification / Alternative check: Biochemical assays uniformly show incorporation in the 5 to 3 direction, and no known cellular DNA polymerase synthesizes 3 to 5. Why Other Options Are Wrong: 3 to 5 synthesis is not observed. Random or organism specific reversal is not supported. A single active site cannot perform simultaneous opposite direction synthesis. Common Pitfalls: Confusing proofreading direction with synthesis direction. Proofreading removes nucleotides 3 to 5, but synthesis still proceeds 5 to 3. Final Answer: 5' to 3'

Question 16

Exonuclease activities of E. coli DNA polymerases II and III  Which activity do Escherichia coli DNA polymerases II and III lack among the listed choices?

Accepted Answer

Introduction: Different DNA polymerases in bacteria specialize in distinct tasks and possess characteristic nuclease activities. Identifying which enzyme has which exonuclease capability clarifies roles in replication versus primer removal and repair. Given Data / Assumptions: Pol I, Pol II, and Pol III are the classic E. coli DNA polymerases. Pol I performs primer removal using a 5 to 3 exonuclease activity. Pol II and Pol III are involved in repair and replication with strong proofreading but without primer removal. Concept / Approach: Pol II and Pol III share a 3 to 5 exonuclease for proofreading misincorporations. Only Pol I has the 5 to 3 exonuclease that degrades RNA primers or damaged DNA ahead of synthesis, a key function during lagging strand maturation. Step-by-Step Solution: 1) Assign replication synthesis to Pol III holoenzyme with 3 to 5 proofreading.2) Assign repair synthesis roles to Pol II with 3 to 5 proofreading as well.3) Assign primer removal to Pol I with 5 to 3 exonuclease.4) Conclude that Pol II and Pol III lack 5 to 3 exonuclease activity. Verification / Alternative check: Genetic and biochemical studies of mutants confirm that loss of 5 to 3 exonuclease maps to Pol I, not Pol II or Pol III. Why Other Options Are Wrong: Pol II and Pol III do have 3 to 5 exonuclease for proofreading, contradicting option E. Endonuclease activities listed are not defining features of these polymerases. Common Pitfalls: Confusing exonuclease directionality or assuming all polymerases remove primers. Remember the division of labor at the replication fork. Final Answer: 5' to 3' exonuclease activity

Question 17

Architecture of the nucleosome  A canonical nucleosome particle is composed of which histone assembly together with approximately how much DNA?

Accepted Answer

Introduction: The nucleosome is the fundamental repeating unit of chromatin. Knowing its composition is essential for understanding DNA accessibility, transcription regulation, and higher order chromosome organization. Given Data / Assumptions: Core histones are H2A, H2B, H3, and H4. DNA wraps around the histone surface in left handed superhelical turns. Linker DNA connects adjacent nucleosomes and varies in length beyond the core particle. Concept / Approach: The nucleosome core particle contains two copies of each core histone, forming an octamer. About 146 base pairs of DNA are tightly wrapped around this octamer in about 1.7 turns, creating a protected core resistant to nucleases relative to linker DNA. Step-by-Step Solution: 1) Assemble histone octamer as (H3 H4)2 tetramer plus two H2A H2B dimers.2) Wrap approximately 146 base pairs of DNA around the octamer surface.3) Recognize that linker DNA and H1 contribute to higher order compaction but are not part of the core particle count.4) Conclude the correct composition and DNA length for a canonical nucleosome. Verification / Alternative check: Micrococcal nuclease digestion yields a protected fragment of about 146 base pairs, a classic experimental signature of the nucleosome core particle. Why Other Options Are Wrong: Options listing tetramer or hexamer do not match the core octameric structure. Three hundred base pairs overstates the core wrapped DNA and confuses core with nucleosome plus long linker. Common Pitfalls: Assuming the protected length widely varies or that H1 is part of the core octamer. H1 is linker associated and not counted in the core particle composition. Final Answer: Histone octamer and about 146 base pairs of DNA

Question 18

DNA melting temperature (Tm) — Within what approximate temperature range do most double-stranded DNA molecules denature under standard laboratory salt conditions?

Accepted Answer

Introduction: The melting temperature (Tm) of DNA is the temperature at which half of a population of double-stranded DNA molecules becomes single-stranded. This question tests fundamental knowledge of nucleic acid thermodynamics and typical laboratory conditions used in molecular biology. Given Data / Assumptions: Standard buffer ionic strength (for example, moderate NaCl concentrations commonly used in the lab). Typical lengths from a few hundred base pairs to genomic fragments. No extreme GC content or unusual solvents unless stated. Concept / Approach: DNA duplex stability depends on base stacking and hydrogen bonding. GC pairs contribute more to stability than AT pairs. Salt stabilizes the duplex by shielding negative charges on the phosphate backbone. Under common conditions, most DNA exhibits a cooperative melting transition with a midpoint (Tm) typically falling in the upper-middle Celsius range, often around 70–90°C for many practical applications (e.g., PCR denaturation, thermal melting curves). Step-by-Step Solution: Identify typical laboratory denaturation practice: PCR routinely denatures DNA near 94–95°C to ensure complete strand separation, but many DNA fragments have Tm values well below that, typically in the 70–90°C range depending on sequence and salt.Recall empirical estimates: short oligonucleotides may use formulas like Tm ≈ 2*(A+T) + 4*(G+C) for rough guidance, while longer DNAs follow salt- and length-dependent equations.Consider that extremely low ranges (e.g., 40–60°C) do not generally melt standard duplex DNA under moderate salt, whereas 80–100°C overshoots for many sequences and conditions.Therefore, the broad, most representative range is 70 to 90°C. Verification / Alternative check: Thermal denaturation profiles recorded by UV absorbance at 260 nm (hyperchromic shift) commonly show sigmoidal transitions with midpoints in this range for average GC content. Changing salt or organic solvents shifts Tm accordingly, but the baseline expectation remains 70–90°C for many samples. Why Other Options Are Wrong: 50 to 60°C / 40 to 55°C: too low for stable duplex DNA at typical salt concentrations. 60 to 80°C: lower bound can be true for AT-rich or short duplexes, but the upper bound omits many common cases; less representative than 70–90°C. 80 to 100°C: upper portion includes boiling; many DNAs melt well before 100°C. Common Pitfalls: Assuming one fixed Tm for all DNA. Tm shifts with GC content, length, salt, and additives (e.g., formamide lowers Tm). Always interpret ranges as typical, not absolute. Final Answer: 70 to 90°C.

Question 19

Semi-conservative replication evidence — In the Taylor, Woods, and Hughes autoradiography of Vicia faba, DNA was synthesized in radioactive thymidine during S phase. After one S phase, what labeling pattern was seen for sister chromatids?

Accepted Answer

Introduction: Classic experiments in chromosome autoradiography provided direct visual evidence for semi-conservative DNA replication. This question revisits the Taylor, Woods, and Hughes study using Vicia faba (broad bean), in which cells incorporated radioactive thymidine during S phase to track newly synthesized DNA strands. Given Data / Assumptions: Cells were exposed to tritiated thymidine during one S phase. Autoradiography detects newly synthesized DNA strands as labeled regions. Semi-conservative model: each daughter duplex contains one parental and one newly made strand. Concept / Approach: When replication is semi-conservative and labeling occurs during the entire S phase, each newly synthesized strand in both sister chromatids will be radioactive. Each chromatid contains one parental unlabeled strand and one labeled nascent strand, so both chromatids show labeling over their lengths in autoradiographs. Step-by-Step Solution: Label incorporated during S phase → every new strand synthesized in that cycle is radioactive.Semi-conservative outcome → each sister chromatid receives one new (labeled) strand paired with one old (unlabeled) strand.Therefore, both chromatids of each replicated chromosome appear labeled after that S phase.In a subsequent unlabeled S phase, only one chromatid would remain labeled, matching further semi-conservative expectations. Verification / Alternative check: Meselson–Stahl density-gradient results are consistent with this logic: after one replication, hybrids are formed; autoradiography simply visualizes nascent strand incorporation directly at the chromosomal level. Why Other Options Are Wrong: Only one chromatid labeled: would imply conservative or partial labeling protocols; not the outcome with labeling throughout S phase. Neither labeled: contradicts the experimental setup. Both (a) and (b): mutually exclusive in this context. Only centromeres labeled: labeling was genome-wide where synthesis occurred. Common Pitfalls: Confusing the pattern after the first labeled S phase with that after a second, unlabeled S phase, when a single chromatid per chromosome retains label. Final Answer: both chromatids of a chromosome were labeled.

Question 20

DNA replication models — In a cesium chloride density gradient experiment (à la Meselson–Stahl), what bands are observed after two rounds of replication in light medium?

Accepted Answer

Introduction: The Meselson–Stahl experiment used cesium chloride density gradients to distinguish conservative, semi-conservative, and dispersive DNA replication. This question asks you to recall the predicted banding pattern after two generations in light (14N) medium following initial growth in heavy (15N) medium. Given Data / Assumptions: Gen 0 DNA is heavy (15N). Cells are shifted to light (14N) medium. Semi-conservative replication is assumed. Concept / Approach: After one replication in 14N medium, all DNA is hybrid (one heavy strand + one light strand), producing a single medium band. After two replications, half the molecules are hybrid (medium) and half are fully light, giving two bands: one medium and one light, with no heavy DNA remaining. Step-by-Step Solution: Generation 1: heavy → hybrid (medium band only).Generation 2: hybrids replicate to produce 50% light–light and 50% hybrid → two bands (light and medium).No heavy–heavy molecules persist after replication in light medium.Therefore, the observed pattern is one light and one medium band. Verification / Alternative check: Quantitative densitometry of the gradient shows increasing light fraction with successive generations, matching semi-conservative predictions and ruling out conservative or dispersive models under these conditions. Why Other Options Are Wrong: Including a heavy band: impossible after replication exclusively in light medium. One medium band only: correct for one generation, not two. Three bands: not predicted by semi-conservative replication at two generations. Two heavy bands: not biologically plausible here. Common Pitfalls: Mixing up the first and second generation patterns; remember: 1st → medium only, 2nd → medium + light. Final Answer: One light and one medium band.

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