Question 1

Protein synthesis fundamentals: In standard cellular translation, where does initiation begin in relation to the mRNA sequence?

Accepted Answer

Introduction / Context: Translation is the process by which ribosomes synthesize proteins from mRNA. Knowing the precise initiation site is key to understanding reading frames, initiation factors, and start-site selection. Given Data / Assumptions: We consider canonical translation in prokaryotes and eukaryotes. Start codon is generally AUG (encoding methionine; formyl-methionine in bacteria), though rare alternatives exist. DNA replication terminology (fork, lagging strand) is unrelated to translation. Concept / Approach: Ribosomes identify the start codon on mRNA: via Shine–Dalgarno interaction in bacteria or scanning from the 5' cap in eukaryotes. Initiation codon establishes the reading frame, after which elongation proceeds codon by codon. Step-by-Step Solution: Define initiation: assembly of ribosomal subunits at start codon.Position on mRNA determines peptide reading frame.Therefore, translation begins at the start codon. Verification / Alternative check: Mutation or removal of the start codon prevents proper initiation; reintroduction restores translation. Why Other Options Are Wrong: Replication fork/lagging strand: DNA replication, not translation. “In nucleus”: eukaryotic translation occurs in cytoplasm (or on ER-bound ribosomes); mitochondrial translation occurs in mitochondria. Common Pitfalls: Confusing transcription initiation sites (promoters) with translation start codons. Final Answer: at the start codon

Question 2

DNA complementarity and orientation: If one DNA strand has the sequence 5′-ATTGCCA-3′, what is the 5′→3′ sequence of the complementary strand?

Accepted Answer

Introduction / Context: Working with DNA requires careful attention to base pairing and antiparallel strand orientation. Many exam errors occur from writing complements without reversing orientation. Given Data / Assumptions: Given strand: 5′-ATTGCCA-3′. Complementary base pairing: A–T and G–C. Complement strands are antiparallel: 5′→3′ pairs with 3′→5′. Concept / Approach: First write the complement in the opposite direction (3′→5′), then reverse it to express in the conventional 5′→3′ orientation. This avoids orientation mistakes and ensures correctness. Step-by-Step Solution: Given: 5′-A T T G C C A-3′.Complement (3′→5′): 3′-T A A C G G T-5′.Write complement 5′→3′ by reversing: 5′-T G G C A A T-3′.Thus, the answer is 5′-TGGCAAT-3′. Verification / Alternative check: Align antiparallel strands and verify each base pair: A–T, T–A, T–A, G–C, C–G, C–G, A–T. Why Other Options Are Wrong: 5′-TAACGGT-3′ is the complement written in the wrong 5′→3′ direction for the opposite strand. Repeating the same strand is incorrect. RNA option with U is irrelevant to DNA complement. Common Pitfalls: Forgetting to reverse the direction after complementing; substituting U for T. Final Answer: 5′ TGGCAAT 3′

Question 3

Gene regulation in bacteria: The catabolite activator protein (CAP, also called CRP) exemplifies which control mode of transcription?

Accepted Answer

Introduction / Context: Bacterial transcription is regulated by repressors and activators. CAP (CRP) integrates carbon source availability (via cAMP) to upregulate genes like the lac operon when glucose is scarce. Given Data / Assumptions: CAP binds DNA with cAMP and enhances RNA polymerase recruitment. We distinguish positive control (activation) from negative control (repression). Focus is classic E. coli paradigms. Concept / Approach: In positive control, regulatory proteins increase transcription when bound. CAP–cAMP binds upstream of target promoters, stabilizing RNA polymerase–promoter interactions and boosting transcription initiation. Step-by-Step Solution: Identify CAP function: transcriptional activator.Relate to mechanism: CAP–cAMP enhances RNAP binding.Therefore, CAP is positive control. Verification / Alternative check: In high glucose, cAMP levels fall, CAP activation decreases; lac operon transcription drops—consistent with activator logic. Why Other Options Are Wrong: Negative control: involves repressors blocking transcription (e.g., LacI), not CAP. “Second type” is vague and not standard nomenclature. “None” is incorrect because CAP clearly activates. Common Pitfalls: Confusing CAP with LacI; remembering that operon output requires both derepression (allolactose) and activation (CAP–cAMP) for full expression. Final Answer: positive control of gene expression

Question 4

Degeneracy of the genetic code: Which codon pair best illustrates that different codons can specify the same amino acid (i.e., degeneracy)?

Accepted Answer

Introduction / Context: The genetic code is degenerate, meaning most amino acids are encoded by more than one codon. Recognizing synonymous codons is crucial for translation, codon optimization, and understanding mutations. Given Data / Assumptions: Standard genetic code (not mitochondrial variants). We seek pairs that encode the same amino acid. Stop codons and start codon roles are considered. Concept / Approach: CAU and CAC both encode histidine, demonstrating degeneracy. By contrast, UAA is a stop codon and UAC encodes tyrosine; AUG encodes methionine (start) while AUA encodes isoleucine; UUA encodes leucine while UUC encodes phenylalanine. Step-by-Step Solution: Check each pair against the codon table.Identify synonymous pair: CAU ↔ CAC → histidine.Therefore, select CAU and CAC. Verification / Alternative check: Any codon table confirms His = CAU/CAC; Tyr = UAU/UAC; Stop = UAA/UAG/UGA; Met = AUG; Ile = AUU/AUC/AUA. Why Other Options Are Wrong: UAA/UAC: stop vs tyrosine. AUG/AUA: methionine vs isoleucine. UUA/UUC: leucine vs phenylalanine. Common Pitfalls: Assuming similarity in two-letter prefixes guarantees the same amino acid; third-position wobble does not always ensure synonymy. Final Answer: CAU and CAC

Question 5

Genetic code in bacteria: In prokaryotic translation, what amino acid does the start codon AUG encode, particularly at initiation?

Accepted Answer

Introduction / Context: The genetic code uses nucleotide triplets (codons) to specify amino acids during translation. While AUG commonly codes for methionine, in bacteria the initiating methionine is chemically modified. Understanding this nuance is essential in microbiology, molecular biology, and interpreting N-termini of prokaryotic proteins. Given Data / Assumptions: The codon under consideration is AUG. The context is prokaryotic (bacterial) protein synthesis. Initiation versus internal codon usage may differ. Concept / Approach: In bacteria, the initiator tRNA is tRNAfMet, which carries methionine that is enzymatically formylated to produce N-formyl methionine (fMet). Thus, when AUG serves as the start codon, the first incorporated residue is fMet. Internal AUG codons (not used for initiation) specify unmodified methionine via elongator tRNAMet. Step-by-Step Solution: Identify codon: AUG (commonly “start” and methionine codon).Identify biological system: prokaryotes (bacteria).Recall initiator tRNA: tRNAfMet delivers formylated methionine at initiation.Conclude: At initiation, AUG encodes N-formyl methionine in prokaryotes. Verification / Alternative check: The presence of peptide deformylase and methionine aminopeptidase in bacteria, which remove the formyl group and sometimes the initiator residue post-translationally, corroborates that initiation starts with fMet. Why Other Options Are Wrong: Methionine: true for internal AUG or eukaryotic initiation, but not for bacterial initiation. A stop signal: stops correspond to UAA, UAG, UGA; AUG is not a stop. Alanine: coded by GCU, GCC, GCA, GCG, not AUG. Common Pitfalls: Assuming AUG always inserts the same unmodified methionine; initiation context and organism matter. Also, post-translational removal can hide the original fMet in mature proteins. Final Answer: N-formyl methionine

Question 6

Origin-of-life evidence: Which observation supports the idea that primitive life predated both DNA and protein enzymes?

Accepted Answer

Introduction / Context: The “RNA world” hypothesis proposes that early life relied on RNA for both information storage and catalysis before the evolution of DNA genomes and protein enzymes. Evaluating the evidence behind this idea is a common concept in molecular evolution. Given Data / Assumptions: Question asks for evidence that primitive life lacked DNA and enzymes. Modern biochemistry shows RNA molecules (ribozymes) can catalyze reactions. Ribosomal RNA actively catalyzes peptide bond formation. Concept / Approach: RNA can serve dual roles: genetic template and catalyst. Laboratory-selected ribozymes exhibit polymerase, ligase, and peptidyl transferase-like activities. This dual capacity supports a phase where RNA alone sustained heredity and metabolism. Step-by-Step Solution: Identify the statement that directly evidences a pre-DNA, pre-protein world.Recognize that RNA’s catalytic and informational roles satisfy both requirements.Reject claims that are factually incorrect about modern cells. Verification / Alternative check: Ribosomes are ribozymes (the peptidyl transferase center is rRNA). Self-splicing introns and hammerhead ribozymes further confirm catalytic RNA. Why Other Options Are Wrong: DNA and enzymes only in advanced cells: false; even bacteria have DNA and enzymes. Advanced cells lack RNA: false; all cells use RNA (mRNA, tRNA, rRNA). “All of the above”: cannot be correct because the other statements are false. Common Pitfalls: Conflating “evidence for RNA world” with statements about absence of DNA/RNA in modern organisms. The hypothesis relies on RNA’s capacities, not on modern cells lacking DNA or RNA. Final Answer: RNA can both store genetic information and catalyze chemical reactions

Question 7

Genetic code terminology: Codons that do not specify any amino acid are called what in molecular genetics?

Accepted Answer

Introduction / Context: The genetic code includes sense codons (coding for amino acids) and nonsense codons that signal the end of translation. Recognizing stop codons is critical for interpreting open reading frames and designing expression constructs. Given Data / Assumptions: Nonsense/stop codons are UAA, UAG, and UGA. They do not encode an amino acid but recruit release factors. Question asks for the correct term describing such codons. Concept / Approach: “Termination codons” or “stop codons” halt elongation by promoting peptide release from the ribosome. “Initiation” refers to start, not stop, and “propagation” is not standard terminology in the code. Step-by-Step Solution: Identify codons without amino acids: UAA, UAG, UGA.Recall accepted term: termination or stop codons.Choose the option stating “Termination codons (stop codons).” Verification / Alternative check: Genome annotation pipelines define ORFs from start to the first in-frame stop codon, confirming usage of the term. Why Other Options Are Wrong: Initiation codons: AUG (and rarely GUG/UUG) mark start, not stop. Propagation codons: not a standard term in genetics. None: incorrect because a standard term exists. Common Pitfalls: Confusing “nonsense mutation” (creating a stop codon) with missense/silent changes; ensure terminology is precise. Final Answer: Termination codons (stop codons)

Question 8

Start signal: The AUG codon, which codes for methionine, plays what specific role at the beginning of translation?

Accepted Answer

Introduction / Context: Translation begins at a defined start codon that sets the reading frame. In nearly all organisms, AUG serves this role, coding for methionine (Met) or N-formyl methionine (fMet) in bacteria. Given Data / Assumptions: AUG specifies methionine. At initiation, special initiator tRNAs recognize AUG at the ribosomal P site. Question asks for AUG’s functional role at the start. Concept / Approach: AUG functions as the initiation codon, defining the reading frame and recruiting initiation factors and the initiator tRNA. Subsequent AUGs within the frame are read by elongator tRNAs during elongation. Step-by-Step Solution: Identify AUG as the canonical start codon.Link to function: positions the ribosome to begin polypeptide synthesis.Select “Initiation codon (start signal).” Verification / Alternative check: Kozak (eukaryotes) and Shine–Dalgarno (prokaryotes) sequences help position AUG for initiation, reinforcing its role. Why Other Options Are Wrong: Elongation codon: elongation uses many sense codons, but “initiation” is specific. Termination: stop codons are UAA/UAG/UGA. Propagation: non-standard term. Common Pitfalls: Assuming every AUG is a start codon; context and signals determine whether an AUG initiates translation. Final Answer: Initiation codon (start signal)

Question 9

Bacterial initiation: During protein synthesis in prokaryotes, what is the identity of the initiating amino acid delivered by the initiator tRNA?

Accepted Answer

Introduction / Context: Initiation differs between bacteria and eukaryotes. The initiator residue in bacteria is chemically distinct, which has implications for immune recognition, proteomics, and antibiotic targeting. Given Data / Assumptions: System: prokaryotes (e.g., Escherichia coli). Initiator tRNA is tRNAfMet. The first residue is often removed or deformylated post-translationally. Concept / Approach: Bacteria charge the initiator tRNA with methionine and then formylate it, producing N-formyl methionine (fMet). This fMet is inserted when AUG functions as the start codon. Step-by-Step Solution: Identify prokaryotic initiator system.Recall biochemical modification: formyl group added to methionine.Conclude the initiating amino acid is N-formyl methionine. Verification / Alternative check: Enzymes peptide deformylase and methionine aminopeptidase remove the formyl group and sometimes the initial residue; this processing validates the starting presence of fMet. Why Other Options Are Wrong: Methionine: correct for eukaryotic initiation; in bacteria it is formylated. Phenylalanine: coded by UUU/UUC, unrelated to initiation. None: a defined initiating residue exists. Common Pitfalls: Equating bacterial and eukaryotic initiation chemistry; they differ in initiator tRNAs and modifications. Final Answer: N-formyl methionine

Question 10

Mitochondrial and chloroplast codes: In some eukaryotic organelles, how does the genetic code compare to the standard bacterial code?

Accepted Answer

Introduction / Context: The genetic code is nearly universal, but notable exceptions occur in organelles such as mitochondria (and some chloroplasts). Recognizing these deviations is important in genomics and interpreting organelle-encoded proteins. Given Data / Assumptions: Certain mitochondrial genomes reassign codons (e.g., UGA as tryptophan in human mitochondria). Start and stop assignments may differ. Question asks if organelle codes differ from prokaryotic standard. Concept / Approach: Organelle translation systems evolved specialized tRNAs and factors, leading to codon reassignments. Hence, their codes differ from the canonical bacterial code, even though many codons are the same. Step-by-Step Solution: Recall examples of codon reassignment (e.g., AUA as methionine in mitochondria).Note that “nearly universal” allows exceptions.Select the option indicating difference from prokaryotes. Verification / Alternative check: Translation tables (e.g., NCBI genetic codes) list multiple alternative codes for mitochondria and some nuclear lineages. Why Other Options Are Wrong: Exactly the same: contradicted by known reassignments. Partially the same but identical: internally inconsistent. None: a clear, accurate statement exists. Common Pitfalls: Assuming “universal” means no exceptions; in practice, exceptions are critical in sequence annotation. Final Answer: It differs from that used in prokaryotes

Question 11

Decoding the first codon: Which experimental approach did Nirenberg and Matthaei (1961) use to determine that UUU codes for phenylalanine?

Accepted Answer

Introduction / Context: Cracking the genetic code began with cell-free translation experiments. Nirenberg and Matthaei famously used synthetic RNA polymers to show which codons specify which amino acids. Given Data / Assumptions: Poly-U RNA directs incorporation of phenylalanine into polypeptides. Experiment performed in a cell-free E. coli extract with radiolabeled amino acids. Question asks which technique revealed the first codon assignment. Concept / Approach: A homopolymer (poly-U) mRNA was added to a translation extract. Only phenylalanine was incorporated into the newly synthesized protein, proving that UUU encodes Phe. Step-by-Step Solution: Prepare a cell-free translation system.Add synthetic poly-U mRNA.Measure incorporation of radiolabeled phenylalanine; observe strong incorporation specific to UUU. Verification / Alternative check: Subsequent use of poly-A and poly-C corroborated assignments (Lys for AAA, Pro for CCC), and mixed copolymers refined the code later. Why Other Options Are Wrong: Ribosome binding without translation: used later for codon–anticodon binding studies, not the first discovery. Mixed copolymers: were later refinements by Nirenberg and Khorana’s group. None: the poly-U experiment is the correct historical answer. Common Pitfalls: Confusing the timeline of genetic code elucidation; separate milestones involved different techniques. Final Answer: In vitro synthesis of a polypeptide using a poly-U (UUUUU...) RNA template

Question 12

Reading a coding sequence: For the RNA 5′-GAU GGU UGA UGU-3′, how many amino acids are translated before termination (standard code, single reading frame)?

Accepted Answer

Introduction / Context: Decoding an mRNA requires grouping nucleotides into codons and applying the standard genetic code, including recognition of stop codons that terminate translation. Given Data / Assumptions: Sequence is 5′-GAU GGU UGA UGU-3′. Translation starts at the first codon shown and proceeds in-frame. Standard genetic code applies; no reinitiation after a stop. Concept / Approach: Translate codons left to right: GAU, GGU, UGA, UGU. GAU codes Aspartate; GGU codes Glycine; UGA is a stop signal; translation halts upon encountering UGA, so codons after the stop are not translated. Step-by-Step Solution: Group into codons: GAU | GGU | UGA | UGU.Apply code: GAU → Asp; GGU → Gly.Encounter UGA → stop; terminate translation.Count amino acids produced before stop: 2 (Asp, Gly). Verification / Alternative check: Check a codon table: UGA is one of the three termination codons (UAA, UAG, UGA). No further elongation occurs after a stop in a single continuous ORF. Why Other Options Are Wrong: One: ignores the first two sense codons. Three or Four: incorrectly translate past the stop codon. Common Pitfalls: Reading out of frame, forgetting that translation stops at the first in-frame stop, or assuming reinitiation within the same short stretch. Final Answer: Two

Question 13

Combinatorics of the code: With four RNA bases taken three at a time, how many distinct codons exist in the standard genetic code?

Accepted Answer

Introduction / Context: Codons are triplets of nucleotides formed from four bases (A, U, G, C). Counting possible combinations is a basic question linking combinatorics and molecular biology. Given Data / Assumptions: Four symbols (A, U, G, C). Ordered triplets (position matters). Repetition allowed. Concept / Approach: The number of ordered triplets with repetition from a set of four is 4^3. This yields the total number of possible codons recognized by the translation machinery. Step-by-Step Solution: Compute combinations with order and repetition: 4^3.Calculate: 4^3 = 4 * 4 * 4 = 64.Interpretation: 61 sense codons for amino acids plus 3 stop codons in the standard code. Verification / Alternative check: Genetic code tables list 64 entries, confirming the combinatorial calculation. Why Other Options Are Wrong: 3: confuses number of bases with number of codons. 20: number of standard amino acids, not codons. Infinite: the triplet code yields a finite set of combinations. Common Pitfalls: Mixing up amino acid count with codon count; forgetting that multiple codons can encode the same amino acid (degeneracy). Final Answer: 64

Question 14

Wobble and degeneracy: Codons that specify the same amino acid usually differ in which nucleotide position?

Accepted Answer

Introduction / Context: The genetic code is degenerate: most amino acids are encoded by more than one codon. The “wobble” hypothesis explains how a single tRNA can recognize multiple codons, typically differing at the third nucleotide. Given Data / Assumptions: Coding is by triplets, positions numbered 1–3 from 5′ to 3′. tRNA anticodon pairing allows flexibility at the 3′ codon position. Question asks which position typically varies among synonymous codons. Concept / Approach: Because base pairing at the third codon position (5′ anticodon first position) is less stringent, many synonymous codons differ only in this “wobble” position, maintaining the same amino acid assignment while tolerating mutations. Step-by-Step Solution: Review synonymous sets (e.g., GGU/GGC/GGA/GGG for glycine).Observe variation mainly in the third base.Select “Third base (wobble position)” as the correct choice. Verification / Alternative check: Codon tables across amino acids confirm third-position variability; exceptions (e.g., Ile AUA/AUC/AUU) still follow third-base differences. Why Other Options Are Wrong: First or second base changes often alter the amino acid class or polarity and are less commonly synonymous. “None of these” contradicts widely accepted wobble rules. Common Pitfalls: Assuming all positions are equally variable without considering pairing rules; second position often correlates with amino acid hydrophobicity class. Final Answer: Third base (wobble position)

Question 15

Genetic code logic: Crick showed that codons consist of three bases and proposed degeneracy of the code. Which experimental strategy did he use to infer triplets and degeneracy?

Accepted Answer

Introduction / Context: Understanding how nucleotide sequences encode amino acids was a central question in early molecular genetics. Francis Crick and colleagues used specific genetic experiments to deduce that the genetic code is read in non-overlapping triplets and that multiple codons can specify the same amino acid (degeneracy). Given Data / Assumptions: The question asks which method Crick used to infer triplet codons and degeneracy. Historically relevant approaches included mutational analysis in phage systems. Frameshift mutations change the reading frame unless compensated. Concept / Approach: If codons are read in groups of three, adding or deleting one nucleotide will shift the reading frame and scramble downstream protein sequence. However, adding or deleting three nucleotides may restore the original frame. Observing suppression of the mutant phenotype by compensating insertions or deletions provides strong evidence for a triplet code. Step-by-Step Solution: Identify Crick’s key experiment → mutational analysis using proflavin to induce single-base insertions or deletions. Reason: 1 or 2 base changes cause frameshift and loss of function; 3 base changes restore reading frame and function. Triplet inference arises because three-base sets preserve codon boundaries. Degeneracy inference follows from mapping multiple codons to the same amino acid without altering protein function. Verification / Alternative check: Complementary experiments by Nirenberg, Khorana and others later directly assigned codons to amino acids, confirming triplet, non-overlapping, and degenerate features. Why Other Options Are Wrong: Gel electrophoresis and density gradients can separate molecules but do not reveal codon size; restriction digests and structural techniques didn’t infer triplet logic; X-ray crystallography of ribosomes came much later. Common Pitfalls: Confusing triplet inference (genetic) with later biochemical decoding; assuming any DNA technique from that era addresses codon length directly. Final Answer: Frameshift mutagenesis.

Question 16

Scope of the genetic code: Which statement best describes how universal the genetic code is across organisms?

Accepted Answer

Introduction / Context: The genetic code maps 64 codons to 20 amino acids and stop signals. Its near-universality underpins molecular biology techniques such as cloning, heterologous expression, and comparative genomics. Given Data / Assumptions: Standard code applies broadly across life. Some organelles and lineages show rare deviations. Question asks for the most accurate characterization. Concept / Approach: While most organisms use the standard code, certain mitochondria (e.g., vertebrate mitochondria) and a few protozoa reassign specific codons (for example, UGA coding for tryptophan in mitochondria). These are notable but limited exceptions. Step-by-Step Solution: Identify the dominant rule → standard genetic code is widespread. Recall known exceptions → mitochondrial and select protozoan codon reassignments. Choose the statement that acknowledges near universality with rare exceptions. Verification / Alternative check: Databases list variant codes (mitochondrial, ciliate, etc.), all representing small deviations from the canonical mapping. Why Other Options Are Wrong: Strict universality ignores documented exceptions; species-specific or kingdom-specific claims contradict extensive cross-kingdom conservation; eukaryote-only usage is incorrect. Common Pitfalls: Overgeneralizing exceptions as the rule; assuming variant codes are widespread across all genes and tissues. Final Answer: Universal except for rare exceptions in mitochondria and some protozoa.

Genetic Code and Regulation Questions