Question 1

DNA damage and direct repair Ultraviolet (UV)–induced thymine dimers in DNA can be directly reversed with the help of visible light by which repair process?

Accepted Answer

Introduction / Context: UV radiation creates cyclobutane pyrimidine dimers (most commonly thymine dimers) that distort the DNA helix and block polymerases. Cells deploy several repair pathways; among them, photoreactivation is a unique, light-dependent direct reversal mechanism mediated by photolyase enzymes. Given Data / Assumptions: Damage type: UV-induced thymine dimers. Some organisms possess photolyase; others (including placental mammals) do not. Visible light is required to activate photolyase for direct reversal. Concept / Approach: Photoreactivation uses a DNA photolyase that absorbs visible light and uses that energy to cleave the cyclobutane ring linking adjacent thymines, restoring normal base pairing without excising nucleotides. This contrasts with nucleotide excision repair, which removes a short stretch of damaged DNA and fills the gap by synthesis. Step-by-Step Solution: Identify damage: thymine dimers caused by UV.Recall direct reversal pathway: photoreactivation using photolyase.Note requirement: visible light provides energy for the reaction.Select “Photoreactivation.” Verification / Alternative check: Genetic studies show organisms lacking photolyase rely more heavily on excision repair and exhibit higher UV sensitivity in the absence of light-mediated repair. Why Other Options Are Wrong: Phosphorylation: protein modification, not DNA lesion reversal. Excision repair: removes and resynthesizes rather than directly reversing the dimer. Photosynthesis: energy-harvesting process, unrelated to DNA repair. Translesion synthesis: bypasses lesions, does not repair them. Common Pitfalls: Assuming all UV repair is excision-based; photoreactivation is a distinct light-driven pathway when photolyase is present. Final Answer: Photoreactivation.

Question 2

Genetic code disruptions – outcomes of a nonsense mutation A nonsense mutation in a coding region most typically results in which consequence for the polypeptide product?

Accepted Answer

Introduction / Context: Mutations that alter coding sequences can change protein sequence or length. Among these, nonsense mutations convert a sense codon into a stop codon (UAA, UAG, UGA), with major consequences for protein synthesis and function. Given Data / Assumptions: Nonsense mutation introduces an early termination signal. Translation machinery halts at premature stop codon. mRNA quality-control mechanisms (e.g., nonsense-mediated decay) may decrease mRNA levels. Concept / Approach: When a nonsense mutation arises, ribosomes terminate translation prematurely, yielding a truncated protein often unstable or nonfunctional. This is distinct from missense mutations (single amino acid substitutions) and frameshifts (reading-frame disruptions that change length and sequence downstream). Step-by-Step Solution: Define nonsense mutation: codon → stop codon.Infer outcome: early translation termination.Predict product: shortened (truncated) polypeptide.Select the option describing premature termination. Verification / Alternative check: Clinical genetics frequently links nonsense variants to loss-of-function phenotypes due to truncated proteins or reduced mRNA via surveillance pathways. Why Other Options Are Wrong: Abnormal elongation: would require readthrough or frame changes, not nonsense per se. Large in-frame deletion: a structural DNA change, not a single base substitution causing stop. mRNA modification: not the typical effect of a nonsense mutation. Single amino acid substitution: describes missense, not nonsense. Common Pitfalls: Confusing nonsense with missense; assuming all premature stops always yield stable truncated proteins (many are degraded). Final Answer: A premature termination of the synthesis of a polypeptide.

Question 3

Expression vectors for bacterial overproduction In a protein overexpression plasmid designed for bacteria, the promoter driving the cloned gene is typically:

Accepted Answer

Introduction / Context: Expression vectors used to overproduce proteins in bacteria rely on powerful, well-characterized bacterial promoters to achieve high transcription levels and tight control. Selecting the correct promoter type is critical for yield, solubility, and host viability. Given Data / Assumptions: Goal: overproduce a heterologous protein in a bacterial host. Promoters must be recognized by bacterial RNA polymerase (or phage polymerases expressed in bacteria). Tight regulation is often needed to avoid toxicity. Concept / Approach: Common bacterial expression systems use strong promoters such as T7 (driven by T7 RNA polymerase in hosts like BL21(DE3)), tac/trc (hybrids of trp and lac), lac, or arabinose-inducible araBAD. These are specifically optimized for bacterial machinery and frequently inducible for control. Using a gene’s native promoter is uncommon for overexpression because it may be weak or poorly regulated in the host. Cross-kingdom promoter compatibility is generally poor without engineered hybrid systems. Step-by-Step Solution: Identify the host: bacteria require bacterial or phage-derived promoters recognized in bacteria.Recognize the need for strength and regulation.Select the option describing a bacterial (often inducible) promoter as standard. Verification / Alternative check: Widely used systems (e.g., T7/lac operon control in BL21(DE3)) exemplify this approach and are standard in molecular cloning labs and industry. Why Other Options Are Wrong: Dual expression in bacteria and mammalian cells with the same promoter is atypical. “Not regulated” is inaccurate; most systems are inducible. Native promoters often underperform and are less controllable. Eukaryotic TATA promoters are not directly functional in bacteria without extensive engineering. Common Pitfalls: Forgetting the role of host-specific polymerases; assuming a native promoter is sufficient for high-level expression. Final Answer: A bacterial promoter (often strong and regulatable, e.g., T7, tac, trc, lac, araBAD).

Question 4

Mutagenesis mechanisms – sources of frameshifts A frameshift mutation most commonly results from which type of DNA change?

Accepted Answer

Introduction / Context: Frameshift mutations alter the reading frame of a coding sequence, changing every downstream codon. Knowing which DNA lesions cause frameshifts is essential for interpreting mutational spectra and their phenotypic outcomes. Given Data / Assumptions: Frameshifts result from insertions or deletions (indels) of 1 or 2 nucleotides (or any number not divisible by 3). Base modifications like deamination typically cause base substitutions, not frame changes. Pyrimidine dimers distort the helix but do not, by themselves, shift the frame. Concept / Approach: While thymine dimers and deaminations damage DNA, their direct repair or mispairing outcomes generally produce point mutations (transitions/transversions) rather than frameshifts. Frameshifts are classically associated with replication slippage at short repeats or with intercalating agents (e.g., acridines) that promote single-base indels. Step-by-Step Solution: Define frameshift: a shift in the triplet reading frame due to indel not divisible by 3.Evaluate listed lesions: thymine dimer (helix distortion), C→U deamination (transition), G→xanthine (mispairs)—none inherently insert/delete nucleotides.Conclude that “none of the above” is correct; frameshifts arise from indels. Verification / Alternative check: Classic experiments with acridine dyes showed elevated frameshift frequency through single-base insertions/deletions, validating the indel mechanism. Why Other Options Are Wrong: Thymine dimer: blocks polymerases; repaired by excision or photoreactivation; not a frame change per se. C→U deamination and G→xanthine: cause base substitutions after replication. Methylation in promoters: regulatory modification, not a coding-sequence frameshift. Common Pitfalls: Equating any DNA damage with frameshift outcomes; only indels alter codon boundaries directly. Final Answer: None of the above changes directly cause a frameshift; frameshifts typically arise from insertions or deletions not in multiples of 3.

Question 5

Milestones in genomics – first bacterial genome sequenced Which bacterial species had its complete genome sequenced first using whole-genome shotgun sequencing?

Accepted Answer

Introduction / Context: The first complete bacterial genome marked a turning point in genomics, enabling comparative studies, pathogen biology insights, and accelerated gene discovery. Recognizing this milestone provides context for modern sequencing technologies and microbial systems biology. Given Data / Assumptions: Question asks for the first fully sequenced bacterial genome. Approach used: whole-genome shotgun sequencing. Several candidate species are listed, many sequenced later. Concept / Approach: Haemophilus influenzae Rd (strain KW20) was published in 1995 as the first complete bacterial genome, using whole-genome shotgun assembly. This achievement demonstrated feasibility for larger genomes and catalyzed the genomics era for diverse microbes. Step-by-Step Solution: Recall key historical date: 1995.Link to species: H. influenzae Rd.Select that species from the options. Verification / Alternative check: Subsequent early genomes included Mycoplasma genitalium and Escherichia coli K-12, but these were published after the H. influenzae milestone. Why Other Options Are Wrong: E. coli, B. subtilis, S. pneumoniae, S. thermophilus: sequenced later than 1995. Common Pitfalls: Confusing first “model” genome (E. coli) with first “completed” genome; model status does not equal earliest sequencing completion. Final Answer: Haemophilus influenzae.

Question 6

First eukaryotic chromosome sequenced What was the first eukaryotic chromosome to be completely sequenced and assembled?

Accepted Answer

Introduction / Context: Sequencing a complete eukaryotic chromosome was a landmark achievement, showcasing strategies for assembling larger, more repetitive genomes compared with bacteria. Yeast, with its compact genome and genetic tools, served as a key model organism for this work. Given Data / Assumptions: Question asks specifically for the first eukaryotic chromosome sequenced. Several plausible eukaryotic chromosomes are listed. Historical sequencing efforts proceeded from simpler to more complex eukaryotes. Concept / Approach: The first fully sequenced eukaryotic chromosome was S. cerevisiae chromosome III, reported in the early 1990s. This project provided a proof of concept for systematic chromosome-by-chromosome approaches that later enabled complete yeast and higher eukaryote genomes. Step-by-Step Solution: Recall organism: baker’s yeast (S. cerevisiae).Recall specific chromosome: chromosome III.Choose the option naming yeast chromosome III. Verification / Alternative check: Human chromosomes (e.g., 22) and plant chromosomes were completed later, after yeast served as a prototype system. Why Other Options Are Wrong: Yeast chromosome XI and Arabidopsis chromosome IV were sequenced later. “None of these” is incorrect because yeast chromosome III fits the historical record. Common Pitfalls: Assuming human chromosomes were first due to notoriety; in reality, simpler eukaryotes led the way. Final Answer: Yeast (Saccharomyces cerevisiae) chromosome III.

Question 7

Using rRNA gene sequences in microbiology Sequencing of rRNA genes (such as 16S rRNA in bacteria or 18S rRNA in eukaryotes) can be used to:

Accepted Answer

Introduction / Context: Ribosomal RNA (rRNA) genes are highly conserved across all domains of life, with variable regions that enable discrimination among taxa. Sequencing these genes underpins molecular taxonomy, microbial ecology surveys, and the initial identification of unknown isolates. Given Data / Assumptions: 16S rRNA (bacteria/archaea) and 18S rRNA (eukaryotes) contain conserved and variable regions. Comparison to curated databases supports identification and phylogeny. Phenotypic traits (e.g., Gram reaction) are not predicted solely from rRNA sequence. Concept / Approach: By aligning an unknown rRNA gene sequence with reference sequences, one can determine its closest relatives and place the organism on a phylogenetic tree. This provides a tentative identification (often to genus, sometimes species) and evolutionary context, but does not directly yield phenotypic characteristics such as cell wall architecture, PFGE banding patterns, or drug susceptibility. Step-by-Step Solution: Amplify rRNA gene (e.g., 16S) using universal primers.Sequence and compare to databases to find nearest neighbors.Use phylogenetic analysis to infer relatedness and tentative identity. Verification / Alternative check: Metagenomic surveys and clinical diagnostics routinely rely on 16S/18S sequencing for culture-independent identification, confirming this application. Why Other Options Are Wrong: Eukaryotes only: incorrect—prokaryotes are a primary use case. PFGE pattern prediction: banding depends on genome restriction sites, not rRNA sequences. Gram reaction prediction: not reliably deduced from rRNA alone. Antibiotic susceptibility: requires phenotypic testing or specific resistance gene detection. Common Pitfalls: Overinterpreting rRNA data as predictive of phenotype; it is primarily taxonomic/phylogenetic. Final Answer: Obtain a tentative identification of a new microorganism and infer its phylogenetic relatedness.

Question 8

Predicting effects on protein length Which type of mutation, by definition, does not change the length (number of amino acids) of the encoded protein?

Accepted Answer

Introduction / Context: Different mutation classes have characteristic impacts on protein sequence and length. Distinguishing these outcomes aids in predicting phenotype and interpreting sequencing results in clinical and research settings. Given Data / Assumptions: Nonsense mutations create premature stop codons, usually shortening proteins. Frameshifts alter the reading frame, almost always changing length and sequence downstream. Missense mutations substitute one amino acid for another without altering the total length. Concept / Approach: A missense mutation is a base substitution that changes one codon to another coding for a different amino acid. Because the number of codons remains the same, the protein length is preserved. By contrast, nonsense and frameshift mutations typically affect length (shortened or altered-length products). Step-by-Step Solution: Define each mutation type and its typical impact on length.Identify the class that leaves length unchanged: missense.Choose “Missense mutation.” Verification / Alternative check: Protein domain analyses often tolerate certain missense changes with preserved length but altered function or stability, aligning with the definition. Why Other Options Are Wrong: Nonsense: truncates the protein early. Frameshift: changes downstream codons and often introduces an early stop, altering length. “All of these”: incorrect because only missense preserves length. Splice-site deletion of an exon: changes length due to exon loss. Common Pitfalls: Confusing “silent” (synonymous) with “missense”; both keep length, but silent does not change the amino acid while missense does. Final Answer: Missense mutation.

Question 9

Strand discrimination in DNA mismatch repair (bacteria) During post-replicative mismatch repair in many bacteria, how are newly synthesized DNA strands distinguished from the parental strands?

Accepted Answer

Introduction / Context: Mismatch repair (MMR) corrects replication errors that escape polymerase proofreading. In bacteria such as E. coli, the system must identify which strand carries the newly introduced error and which is the correct template. Strand discrimination is essential to fix the right base. Given Data / Assumptions: Hemimethylation occurs immediately after replication. Dam methylase methylates adenines in GATC sites on the parental strand first. MMR proteins recognize methylation status to direct repair. Concept / Approach: Right after replication, the parental strand is methylated at GATC sites, while the nascent strand is not yet methylated. The MutS/MutL/MutH system targets the unmethylated (new) strand for incision and resynthesis, thereby correcting the mismatch using the methylated parental strand as the template. Step-by-Step Solution: Recognize hemimethylated DNA as the post-replication state.Identify which strand is methylated: the older template.Conclude MMR discriminates using methylation marks, targeting the unmethylated new strand.Select the option describing “old methylated, new unmethylated.” Verification / Alternative check: Mutations in dam methylase or MutHLS components disrupt strand discrimination and elevate mutation rates, validating the mechanism. Why Other Options Are Wrong: Absence of cytosine or molecular size differences are unrelated to MMR marking. New strands methylated while old are not: reverses the biological reality. Ribonucleotide incorporation is not a normal discrimination signal. Common Pitfalls: Confusing eukaryotic MMR cues (e.g., nicks on the lagging strand) with bacterial methyl-directed MMR; mechanisms differ across domains. Final Answer: Old (template) strands are methylated while the new strands are initially unmethylated (hemimethylated DNA).

Question 10

In classical genetics and evolutionary biology, which statement best describes the nature of genetic variations in a population? Choose the option that reflects their persistence and heritability rather than short lived environmental effects.

Accepted Answer

Introduction / Context: Genetic variation refers to differences in DNA sequences among individuals of a species. These differences arise through mutation, recombination, and other genomic processes and provide the raw material for evolution by natural selection. The key attribute of genetic variation is that it resides in the genotype and is transmissible across generations, making it relatively stable compared with purely environmental or physiological changes. Given Data / Assumptions: The term variation is being used in a genetic sense, not short term physiological acclimation. Heritability implies that the underlying DNA change can pass from parents to offspring. Environmental influences can alter phenotype without altering DNA sequence. Concept / Approach: Mutations that change nucleotide sequences create genetic variants. Once incorporated into germline DNA (or the entire genome in single celled microbes), these variants persist unless removed by counter mutation or selection. Phenotypic traits can be influenced by environment, but unless the DNA itself changes, those effects are not genetic. Therefore, genetic variations are characterized by stability and heritability. Step-by-Step Solution: Identify that genetic variation refers to DNA sequence differences. Connect DNA based differences to inheritance across generations. Contrast with environmental effects that do not alter DNA. Select the option that captures persistence and heritability: stable. Verification / Alternative check: Population genetic models treat allele frequencies as stable quantities that change only via mutation, migration, selection, and drift, underscoring that genetic differences are not merely transient environmental responses. Why Other Options Are Wrong: Temporary: suggests short lived, which contradicts heritable DNA level changes. Influenced by the environment: environment can affect phenotype, but that does not define genetic variation. Not heritable: contradicts the core definition of genetic variation. Common Pitfalls: Confusing epigenetic or physiological acclimation with true genetic change; only sequence level alterations constitute genetic variation in the strict sense. Final Answer: stable

Question 11

In automated DNA sequencing systems based on dye terminator chemistry, how are the four nucleotide bases (A, C, G, T) distinguished during detection?

Accepted Answer

Introduction / Context: Modern capillary and next generation Sanger based sequencing platforms identify nucleotides by fluorescent signals. Understanding how each base is differentiated is fundamental for interpreting chromatograms and troubleshooting runs in molecular diagnostics and genomics labs. Given Data / Assumptions: Automated sequencing relies on labeled nucleotides or terminators. A detector measures signals as fragments migrate past a window. The platform is not using radiolabels or immuno tags. Concept / Approach: In dye terminator sequencing, each dideoxynucleotide terminator (ddATP, ddCTP, ddGTP, ddTTP) carries a spectrally distinct fluorescent dye. As terminated fragments are separated by size in a capillary, a laser excites the dyes and an optical system records emission wavelengths. The instrument software assigns base calls based on the unique fluorescent signature of each dye. Step-by-Step Solution: Recognize that Sanger automation uses fluorescently labeled terminators. Note that each base must have a unique detectable signature. Match this requirement to the use of distinct fluorophores. Select distinctive fluorescent tag as the correct mechanism. Verification / Alternative check: Chromatogram peaks appear in different colors corresponding to A, C, G, and T; spectral deconvolution confirms dye specific identification. Why Other Options Are Wrong: Different radioactive tag: older manual methods used radioactivity, not automated multi color detection. Cytosine at start: irrelevant to base differentiation. Unique antibody: antibodies are not used for base discrimination in sequencing ladders. Common Pitfalls: Confusing dye primer with dye terminator approaches; both rely on fluorescent tags, not antibodies or radioactivity in current automated systems. Final Answer: distinctive fluorescent tag

Question 12

Which class of mutations arises in the absence of deliberate exposure to external mutagenic agents, originating instead from normal cellular processes such as replication errors or spontaneous base alterations?

Accepted Answer

Introduction / Context: Mutations can originate without any intentional treatment. Cells constantly face endogenous sources of DNA change, including replication slippage, tautomeric shifts, oxidative damage, and depurination. Distinguishing spontaneous from induced mutations is a basic classification in genetics and microbial mutagenesis. Given Data / Assumptions: No external physical or chemical mutagens are applied. Endogenous processes are capable of altering DNA. Terminology follows standard genetics usage. Concept / Approach: Spontaneous mutations arise naturally during the life of a cell. DNA polymerases have finite fidelity and, despite proofreading and mismatch repair, occasional errors persist. Hydrolytic reactions such as deamination of cytosine to uracil or depurination create abasic sites; reactive oxygen species can oxidize bases like guanine to 8 oxoguanine, leading to mispairing. These events occur without external triggers. Step-by-Step Solution: Identify that no external agent is present. List endogenous mechanisms that can cause base changes or insertions and deletions. Map the definition to the correct term: spontaneous mutations. Exclude induced mutations which require a mutagen. Verification / Alternative check: Fluctuation tests show mutation occurrence before selection pressure, consistent with spontaneous origin rather than induced change during selection. Why Other Options Are Wrong: Analogous mutations: not a recognized category in this context. Induced mutations: require exposure to mutagens like UV or alkylating agents. None of these: incorrect because a standard term exists. Common Pitfalls: Assuming all mutations are environmentally driven; baseline mutation rates persist due to intrinsic biochemical processes. Final Answer: Spontaneous mutations

Question 13

Ultraviolet light can create thymine dimers in DNA. Among common repair routes, which mechanism is error prone and therefore most likely to introduce new mutations while allowing replication to proceed?

Accepted Answer

Introduction / Context: Thymine dimers are a hallmark of UV damage that can block replication. Cells deploy several repair systems with different accuracies. Understanding which pathway is error prone helps explain mutagenesis after UV exposure and the balance between survival and genome integrity. Given Data / Assumptions: DNA contains UV induced cyclobutane pyrimidine dimers. Multiple repair mechanisms exist in microbes and eukaryotes. Error tolerance varies by pathway. Concept / Approach: Photoreactivation (photolyase mediated) directly reverses dimers using visible light and is considered error free because it restores the original bases. Nucleotide excision repair removes a short oligonucleotide containing the lesion and fills the gap using the opposite strand as a template, typically maintaining fidelity. SOS repair, in contrast, induces specialized translesion synthesis polymerases that can replicate across lesions but lack high fidelity, raising the chance of base substitutions or small insertions and deletions. Step-by-Step Solution: List candidate mechanisms: photoreactivation, excision repair, SOS repair. Classify their fidelity: photoreactivation and excision are largely accurate. Recognize SOS as an inducible, damage tolerant, error prone system. Select SOS repair as most likely to introduce mutations. Verification / Alternative check: Mutator phenotypes with elevated translesion polymerase activity show increased spontaneous mutation rates, validating the error prone nature of SOS responses. Why Other Options Are Wrong: Excision repair: template directed gap filling preserves sequence. Photoreactivation: direct lesion reversal without sequence change. Never leads to mutation: unrealistic, given SOS polymerase properties. Common Pitfalls: Assuming all repair improves fidelity; some pathways prioritize survival over accuracy when damage is extensive. Final Answer: SOS repair

Question 14

Mutations are best characterized as changes occurring in which biological level, while recognizing that visible traits may or may not be altered?

Accepted Answer

Introduction / Context: A mutation is a heritable change in the nucleotide sequence of DNA. Although mutations can lead to altered traits, not every genotype change produces a detectable phenotype due to redundancy, silent substitutions, or buffering by biological networks. Properly distinguishing genotype from phenotype clarifies definitions in genetics and molecular biology. Given Data / Assumptions: Mutation is defined at the level of DNA sequence. Phenotypic change depends on context, dominance, and gene function. Silent and neutral mutations are common. Concept / Approach: The genotype encodes the information; the phenotype is the expressed outcome shaped by genotype and environment. Mutations directly affect genotype. Whether a phenotype changes depends on the specific site and type of mutation and on environmental conditions. Therefore, the defining characteristic of mutations is a change in genotype, not necessarily phenotype. Step-by-Step Solution: Anchor the definition: mutation equals DNA sequence change. Acknowledge that phenotypes may remain unchanged after some mutations. Select the option that identifies genotype as the locus of change. Reject options implying phenotype change is mandatory. Verification / Alternative check: Synonymous codon substitutions do not alter amino acid sequence yet are bona fide mutations; this confirms that phenotype change is not required for mutation classification. Why Other Options Are Wrong: Phenotype: can change, but not required for a mutation to exist. Both: overstates the requirement; phenotype change is not necessary. None: contradicts the genotype based definition. Common Pitfalls: Equating all mutations with disease; many mutations are neutral or context dependent and do not produce obvious phenotypes. Final Answer: Genotype

Question 15

Whole genome shotgun sequencing primarily relies on which core strategy to reconstruct an entire genome efficiently from DNA?

Accepted Answer

Introduction / Context: Genome projects often use shotgun approaches to accelerate sequencing and assembly. The hallmark of shotgun methodology is breaking the genome into many small pieces, sequencing each independently, and then using computational overlap to reconstruct the original sequence. Given Data / Assumptions: Random fragmentation produces overlapping reads. High coverage enables accurate consensus sequence. Assembly software aligns overlaps to build contigs and scaffolds. Concept / Approach: In whole genome shotgun sequencing, DNA is randomly sheared to create numerous fragments. Each fragment is cloned or directly sequenced, generating a large number of short reads. Overlap layout consensus or de Bruijn graph algorithms assemble these reads into longer sequences. The efficiency comes from parallel processing of many small pieces rather than laborious mapping of large clones. Step-by-Step Solution: Identify the essential feature: random fragmentation and massive parallel sequencing. Note that reconstruction depends on overlapping reads with sufficient depth. Match this to the option describing thousands of small randomly cloned fragments. Select the shotgun defining strategy accordingly. Verification / Alternative check: Historical genome projects (for example, bacterial genomes and later larger eukaryotes) demonstrated rapid progress using shotgun approaches with high coverage and computational assembly, validating the core strategy. Why Other Options Are Wrong: Sequencing a few large clones: characteristic of hierarchical methods, not shotgun. Sequencing intact chromosomes: not feasible with standard platforms and not the shotgun principle. All of the above: mixes incompatible strategies. Common Pitfalls: Confusing hierarchical clone by clone mapping with shotgun; the latter emphasizes randomness and scale rather than stepwise mapping. Final Answer: rapidly sequencing thousands of small randomly cloned fragments

Question 16

A nonsense mutation introduces a premature stop codon within a coding sequence. What is the most direct molecular consequence typically observed for the gene product?

Accepted Answer

Introduction / Context: Point mutations can change a sense codon to a stop codon (UAA, UAG, UGA), producing a nonsense mutation. This event halts translation prematurely and often yields nonfunctional or unstable proteins. Recognizing the consequence helps interpret genetic test results and predict phenotypes. Given Data / Assumptions: The stop codon occurs within the open reading frame before the normal termination site. Translation machinery terminates at the premature stop. In some eukaryotes, nonsense mediated decay can reduce mRNA abundance, but the primary direct effect is on translation length. Concept / Approach: The ribosome releases the nascent polypeptide upon encountering a stop codon, so the produced protein is truncated relative to the wild type. Frameshifts require insertion or deletion not in multiples of three, which is distinct from nonsense. While some transcripts may be targeted for degradation by surveillance pathways, the immediate implication is a shortened protein. Step-by-Step Solution: Define nonsense as sense to stop codon conversion. Map ribosome behavior: translation stops at the premature stop. Infer protein outcome: truncated polypeptide. Choose the option describing a shortened protein. Verification / Alternative check: Laboratory expression of nonsense alleles yields shorter bands on immunoblot or absent signal due to instability, consistent with truncation. Why Other Options Are Wrong: Premature termination of the mRNA: transcription termination is not the direct effect. No effect: contradicts the definition. Reading frame shift: caused by indels, not by nonsense substitutions. Common Pitfalls: Confusing transcript degradation (a secondary outcome via surveillance) with the primary translation effect of generating a shortened protein. Final Answer: shorten the length of the protein encoded by the gene

Question 17

Excision repair pathways that correct bulky DNA lesions such as thymine dimers typically include several ordered steps. Which of the following steps are part of the mechanism?

Accepted Answer

Introduction / Context: Nucleotide excision repair removes bulky lesions that distort the DNA helix, including UV induced thymine dimers and certain chemical adducts. The process involves damage recognition, cutting the strand, removing the damaged patch, resynthesis, and sealing. Understanding each step clarifies how integrity is restored. Given Data / Assumptions: Damage distorts the double helix and is recognized by surveillance proteins. Repair enzymes act sequentially to excise and replace the damaged segment. DNA ligase completes the repair by sealing nicks. Concept / Approach: Canonical excision repair includes: incision (endonucleases cut on one or both sides of the lesion), excision (the damaged oligonucleotide is removed), repair synthesis (polymerase fills the gap using the undamaged strand as template), and ligation (DNA ligase seals the final phosphodiester bond). Different organisms have variant protein complexes, but the step logic is conserved. Step-by-Step Solution: Identify incision as endonucleolytic cutting flanking the lesion. Recognize excision as removal of the cut fragment. Acknowledge ligation as the final sealing after gap filling synthesis. Therefore, all listed steps belong to excision repair. Verification / Alternative check: Biochemical reconstitution of excision repair shows distinct incision and excision activities, followed by DNA polymerase and ligase actions to complete repair. Why Other Options Are Wrong: Listing a single step is incomplete; the pathway requires all components. Common Pitfalls: Overlooking the synthesis step mentally; while not listed among the options, it occurs between excision and ligation, but the question focuses on incision, excision, and ligation as core named steps. Final Answer: All of these

Question 18

Choose the correct definition: What is a mutagen in the context of molecular genetics and microbiology?

Accepted Answer

Introduction / Context: Mutagens are central to understanding mutational processes in cells, from environmental exposures to laboratory mutagenesis. Correctly defining a mutagen helps distinguish it from repair enzymes, stabilizers, or regulatory inhibitors, and informs safety practices and experimental design. Given Data / Assumptions: Mutations are heritable DNA sequence changes. External agents can increase mutation frequency above the spontaneous rate. Agents can be physical (for example, UV light) or chemical (for example, alkylating compounds). Concept / Approach: A mutagen is any physical or chemical agent that elevates the rate of mutation by damaging DNA or interfering with replication fidelity. Examples include ultraviolet radiation causing pyrimidine dimers, ionizing radiation causing breaks, and chemicals such as ethyl methanesulfonate introducing alkyl groups that mispair during replication. Step-by-Step Solution: Identify the action: induces or increases mutations. Specify agent types: physical and chemical are both included. Select the option matching this definition precisely. Reject options describing repair or stabilization functions. Verification / Alternative check: Ames test screens chemicals for mutagenicity by measuring reversion rates in reporter strains, demonstrating the operational definition of mutagens. Why Other Options Are Wrong: Enzyme that repairs mutations: describes repair proteins, not mutagens. Inhibitor of gene modification: unrelated to induction of mutations. DNA stabilizer: opposite effect, reducing mutation likelihood. Common Pitfalls: Assuming only chemicals are mutagens; physical agents also qualify and can be potent. Final Answer: a chemical or physical agent that induces mutations

Question 19

Which type of mutation specifically affects only a single nucleotide position within a gene or genome sequence and may result in substitution, insertion, or deletion of one base?

Accepted Answer

Introduction / Context: Mutations can range from single base changes to large chromosomal rearrangements. Single nucleotide changes are among the most common and impactful forms, influencing coding sequences, regulatory elements, and splicing signals. Recognizing the standard term for these events is essential for reading literature and lab reports. Given Data / Assumptions: The mutation affects only one nucleotide position. Possible outcomes include base substitution, or occasionally single base insertion or deletion. Naming follows widely accepted genetic terminology. Concept / Approach: A point mutation is a change at a single nucleotide position. Subtypes include transitions and transversions for substitutions, as well as single nucleotide insertions and deletions that can cause frameshifts if they occur within coding sequences. The term excludes multi nucleotide regional changes and structural variants like inversions or translocations. Step-by-Step Solution: Confirm scope: only one base is altered. Apply the standard term in genetics for single nucleotide changes. Identify that point mutation best fits this description. Eliminate distractors that are nonstandard or overly broad. Verification / Alternative check: Databases such as dbSNP catalog single nucleotide polymorphisms, which are point mutations at the population level, reinforcing the terminology. Why Other Options Are Wrong: Aerial mutation: not a recognized genetic term. Site mutation: vague and nonstandard in this context. Regional mutation: implies a larger affected segment, not a single nucleotide. Common Pitfalls: Equating point mutations only with substitutions; single nucleotide insertions and deletions are also often included when they affect one position. Final Answer: Point mutation

Question 20

Genetics and mutations — When a mutation disrupts vital cellular functions such that the mutated organisms cannot survive or reproduce, this type of mutation is called:

Accepted Answer

Introduction / Context: Mutations can range from silent changes to alterations that fundamentally impair life processes. In genetics and microbiology, it is essential to distinguish between different mutation classes, because each has different biological consequences and implications for viability, inheritance, and disease. Given Data / Assumptions: The question asks about mutations that affect vital functions to the extent that mutants cannot live (nonviable). We compare this definition with other common mutation terms such as nonsense mutation and transversion. We assume standard genetics terminology used in microbiology and molecular biology. Concept / Approach: Mutations are categorized by molecular change (e.g., base substitution, insertion, deletion) or by effect (e.g., silent, missense, nonsense, lethal). A lethal mutation is defined by its phenotypic outcome: it prevents survival or reproduction because an essential gene, pathway, or structural element is compromised. By contrast, a nonsense mutation introduces a stop codon prematurely; it may or may not be lethal depending on the gene. A transversion is a type of base substitution (purine ↔ pyrimidine) and has no inherent lethality without context. Step-by-Step Solution: Identify the key phrase: “mutants are nonviable.”Map this phenotype to the correct term used for outcome-based classification.Select “lethal mutation,” since lethality defines the class regardless of underlying molecular mechanism. Verification / Alternative check: Classic examples include null mutations in genes encoding essential DNA replication proteins or ribosomal components; such mutants cannot form colonies, confirming lethality. Why Other Options Are Wrong: Nonsense mutation: introduces a stop codon; sometimes lethal, sometimes not. Transversion: describes a substitution type, not the viability outcome. None of these: incorrect because “lethal mutation” is the standard term. Common Pitfalls: Equating a specific molecular change (e.g., nonsense) with an outcome (lethality). The same molecular change can be benign or lethal depending on the affected gene. Final Answer: lethal mutation

DNA Sequencing, Mutation and Repair Questions