- A microbiologist identifies two distinct point mutations in the coding sequence of a bacterial enzyme. Mutation 1 changes a GCA codon to a GCG codon. Mutation 2 changes an AAA codon to an AGA codon. (Relevant codons: GCA/GCG = Alanine; AAA = Lysine; AGA = Arginine). Which statement best classifies these two mutations?
Answer: Mutation 1 is a silent mutation, while Mutation 2 is a conservative missense mutation.
Mutation 1 (GCA → GCG) changes the codon but not the encoded amino acid (both code for Alanine); this is a silent mutation. Mutation 2 (AAA → AGA) changes the encoded amino acid from Lysine to Arginine; this is a missense mutation. Because Lysine and Arginine are both basic, positively charged amino acids, it is considered a conservative missense mutation. A neutral mutation refers to the effect on fitness, not the molecular change. A silent mutation is by definition silent at the protein level, while a conservative missense may or may not be neutral with respect to fitness.
- A single guanine deletion occurs at position +7 in the coding sequence of a bacterial gene shown below. The start codon (ATG) is at positions +1 to +3.
5'-ATG GGC TTA GCA CGC TAA-3'
Which of the following describes the most probable consequence for the resulting polypeptide?
Answer: A protein with a radically altered amino acid sequence downstream of the mutation's location.
The original coding sequence is 5'-ATG GGC TTA GCA CGC TAA-3', which translates to Met-Gly-Leu-Ala-Arg-Stop. Deleting the guanine at position +7 (the first G of the GCA codon) results in the new sequence 5'-ATG GGC TAC ACG CTA A..-3'. The reading frame is now shifted. The new codons are ATG (Met), GGC (Gly), TAC (Tyr), ACG (Thr), CTA (Leu), etc. The amino acid sequence is completely different after the second amino acid (Glycine). This is a frameshift mutation. While a premature stop codon might eventually appear in the new frame, the guaranteed and primary consequence is the alteration of the downstream amino acid sequence.
- A researcher analyzes thousands of spontaneous point mutations within the coding regions of the E. coli genome. A strong statistical trend emerges: substitutions in the third position of a codon are far less likely to result in an amino acid change than substitutions in the first or second position. This is a direct consequence of the fact that:
Answer: the genetic code is degenerate, with many amino acids specified by multiple codons differing at this position.
When you encounter questions about mutation patterns in coding sequences, think about how the genetic code's structure affects the impact of different base changes.
The key insight here lies in the degeneracy of the genetic code. Most amino acids are encoded by multiple codons that differ specifically in their third position - this is called "wobble base pairing." For example, leucine is coded by UUA, UUG, CUU, CUC, CUA, and CUG. Notice how the third position can vary widely while still specifying the same amino acid. This means a mutation in the third position often results in a "silent" or "synonymous" mutation that doesn't change the protein sequence.
Answer A correctly identifies this phenomenon - the genetic code's degeneracy, particularly at the third codon position, explains why these mutations are less likely to cause amino acid changes.
Answer B is incorrect because mismatch repair systems don't preferentially target specific codon positions based on their location within codons. These systems recognize structural distortions in DNA, not codon position significance.
Answer C misrepresents DNA polymerase function. The enzyme doesn't have position-specific error rates based on codon structure - it operates at the DNA level without "knowing" about codon boundaries.
Answer D contradicts the observed data. Stop codons are actually less likely to be created by third-position mutations, and the question specifically notes that amino acid changes are less frequent, not that mutations are being selected against.
Remember: the genetic code's redundancy at the third position is evolution's buffer against harmful mutations - a critical concept linking molecular biology to evolutionary fitness.
- A researcher is studying a 1500 bp bacterial gene that codes for a 500-amino-acid polypeptide. Two different nonsense mutations are identified. Mutant 1 has a nonsense mutation in the 10th codon. Mutant 2 has a nonsense mutation in the 490th codon. Which statement most accurately predicts the phenotypes?
Answer: Mutant 1 will likely have a null phenotype, while Mutant 2 may retain partial or full protein function.
When analyzing nonsense mutations, the key factor is where the premature stop codon occurs relative to functional protein domains. The location determines whether any useful protein function can be salvaged.
Mutant 1 has a nonsense mutation at codon 10, producing only the first 9 amino acids before termination. This tiny fragment (less than 2% of the full protein) cannot possibly retain the protein's structure or function - it's essentially a null mutation. Mutant 2, however, has its nonsense mutation at codon 490, allowing production of 489 amino acids (about 98% of the full protein). This near-complete protein may retain partial or even full function if the missing C-terminal region isn't critical for the protein's active site or essential structural elements.
Choice A is wrong because truncation severity depends entirely on location - losing 10 amino acids from the C-terminus is very different from losing 490 from the N-terminus. Choice B incorrectly assumes nonsense-mediated decay will eliminate both transcripts equally. While this quality control mechanism exists in eukaryotes, it's less prominent in bacteria, and even when active, its efficiency varies with mutation position. Choice C reverses the actual relationship - shorter truncated proteins are typically less problematic than longer ones missing critical regions.
The correct answer is D because mutation location determines functional impact: early nonsense mutations create null phenotypes, while late ones may preserve function.
Remember: with nonsense mutations, ask yourself "how much functional protein structure remains?" Early truncations are almost always null; late truncations may retain activity.
- To generate mutants for a genetic screen, a microbiologist treats a culture of Salmonella enterica with ethidium bromide. This chemical is a planar molecule that inserts itself between the stacked bases of a DNA helix. What is the primary type of mutation this treatment is expected to induce?
Answer: Frameshifts, by causing single-base insertions or deletions during DNA replication.
Ethidium bromide is a classic intercalating agent. Its insertion between DNA bases distorts the helix. During replication, this distortion can cause DNA polymerase to either slip and insert an extra base or skip a base entirely. This leads to single-base insertions or deletions, which, in a coding region, result in frameshift mutations. Other mutagens cause transitions/transversions, and UV light causes thymine dimers.
- The coding sequence for a bacterial adhesin protein contains a region with five tandem repeats of the codon GCT (Alanine): ...GCT GCT GCT GCT GCT.... A researcher compares two mutants. Mutant A has a 3-base-pair deletion within this region. Mutant B has a 4-base-pair deletion within this region. What is the most likely outcome for the proteins produced by these mutants?
Answer: Mutant A will produce a slightly shorter but likely functional protein, while Mutant B will produce a nonfunctional protein with an altered C-terminus.
The critical factor is whether the number of deleted bases is a multiple of three. Mutant A has a 3-bp deletion, which removes exactly one codon. This is an in-frame deletion that will result in a protein missing one amino acid (Alanine) but with the correct reading frame downstream. This protein may still be functional. Mutant B has a 4-bp deletion, which is not a multiple of three. This will cause a frameshift mutation, altering the entire downstream reading frame and almost certainly leading to a truncated, nonfunctional protein.
- During DNA replication in E. coli, an adenine base on the template strand undergoes a spontaneous, transient tautomeric shift to its imino form at the moment the replication fork passes. What is the most likely mutation to be incorporated into the newly synthesized strand and subsequently established in the genome after the next round of replication?
Answer: An A:T to G:C transition.
Normally, adenine (A) pairs with thymine (T). The rare imino tautomer of adenine (A*) preferentially base-pairs with cytosine (C). During the first round of replication, the A* on the template strand will cause a C to be incorporated into the new strand, creating an A*:C mismatch. In the second round of replication, this new strand with C will serve as a template, and a guanine (G) will be incorporated opposite it. The final result is that the original A:T base pair has been permanently changed to a G:C base pair, which is a transition mutation.
- A culture of wild-type E. coli lacking a functional nucleotide excision repair (NER) system is briefly exposed to a high dose of ultraviolet (UV) radiation at 260 nm. If the cells attempt to replicate their DNA before the damage is repaired by other means, what is the most common type of mutation that will be permanently incorporated?
Answer: C:G to T:A transitions at dipyrimidine sites.
UV radiation causes the formation of pyrimidine dimers (e.g., T-T, C-T, C-C). When an unrepaired dimer is encountered during replication, error-prone translesion synthesis (TLS) polymerases are recruited as part of the SOS response. These polymerases often misincorporate bases. A very common error is the deamination of a cytosine within a dimer, followed by insertion of an adenine opposite it, leading to a C to T transition. This specific C:G to T:A transition is known as the "UV signature mutation."
- A bacterial enzyme functions as a homotetramer, composed of four identical polypeptide subunits. A specific missense mutation in the subunit gene results in a protein that can still assemble into the tetramer but renders any complex containing even one mutant subunit catalytically inactive. In a hypothetical diploid bacterium heterozygous for this mutation, what would be the expected level of enzyme activity, and what is this type of mutation called?
Answer: <10% activity; an antimorphic (dominant negative) mutation.
This mutation is antimorphic, also known as dominant negative, because the mutant protein product interferes with the function of the wild-type product. In a heterozygote producing 50% wild-type and 50% mutant subunits, the subunits assemble randomly. The probability of forming a tetramer composed of only wild-type subunits is (0.5)4 = 0.0625, or 6.25%. All other combinations will contain at least one mutant subunit and be inactive. Therefore, the total enzyme activity will be severely reduced to less than 10% of the wild-type level. - A mutation occurs in the E. coli gene gltT, which encodes a tRNA for glutamate (tRNA-Glu). The mutation changes the anticodon from 5'-UUC-3' (which recognizes the GAA codon for glutamate) to 5'-UUA-3'. What is the most likely consequence of this mutation?
Answer: The cell will insert the amino acid glutamate at UAA stop codons, producing abnormally long proteins.
When you encounter tRNA mutation questions, focus on the anticodon-codon pairing rules and remember that anticodons are read 3' to 5' while codons are read 5' to 3'.
The mutant tRNA-Glu has anticodon 5'-UUA-3', which pairs with codon 5'-UAA-3' (the amber stop codon). Since the tRNA is still charged with glutamate by the same aminoacyl-tRNA synthetase (which recognizes the tRNA's structure, not its anticodon), this creates a "suppressor" tRNA that inserts glutamate at UAA stop codons. This allows translation to continue past normal termination signals, producing abnormally long proteins with additional amino acids beyond the intended stop point.
Option A correctly describes this suppressor tRNA mechanism. Option B is wrong because the cell still has other functional tRNA-Glu molecules that continue reading GAA codons normally - this mutation affects only one tRNA species out of multiple. Option C misses the point entirely; while redundancy exists for normal glutamate incorporation, this mutant tRNA gains a new, problematic function rather than simply losing its old one. Option D is incorrect because aminoacyl-tRNA synthetases recognize tRNA structure through the acceptor stem and variable regions, not the anticodon, so the tRNA will still be charged with glutamate.
For microbiology exams, remember that suppressor tRNA questions test whether you understand that: (1) tRNA identity for charging depends on structural elements beyond the anticodon, and (2) anticodon mutations can create new codon recognition patterns while maintaining the original amino acid specificity.
- A large chromosomal inversion occurs in a bacterium, flipping a 50-kb segment of DNA that contains several operons. The breakpoints of the inversion do not occur within any coding sequences or promoters. Which of the following is the most likely consequence?
Answer: Minimal phenotypic change, but the altered gene order would be detectable by whole-genome sequencing.
If an inversion does not disrupt any genes or their regulatory elements at its breakpoints, it can be phenotypically silent. All the genes are still present and can be transcribed normally, regardless of their orientation on the chromosome. The primary change is to the gene order on the chromosome. This large-scale rearrangement would not be detected by simple PCR of an internal gene but would be evident from techniques that map gene order, such as whole-genome sequencing or restriction mapping.
- A single base substitution in an E. coli gene changes a tryptophan codon (UGG) to a stop codon (UGA) at position 50 of a 400-amino acid protein. Which of the following accurately describes the primary molecular consequence in this bacterial cell?
Answer: A truncated, 49-amino acid polypeptide will be synthesized, which is likely non-functional.
A nonsense mutation creates a stop codon within the coding sequence. When the ribosome encounters this premature stop codon (UGA), it terminates translation. The result is the synthesis of a shortened, or truncated, polypeptide. In this case, the protein would be 49 amino acids long instead of 400. Nonsense-mediated decay (NMD) is a quality control mechanism primarily found in eukaryotes, not bacteria. The mutation affects translation, not transcription, so the mRNA length is not affected.
- A temperature-sensitive (ts) mutant of a bacteriophage forms plaques on a bacterial lawn at 30°C (permissive temperature) but fails to form plaques at 42°C (restrictive temperature). The most probable molecular explanation for this phenotype is a:
Answer: missense mutation leading to a protein that is conformationally unstable at 42°C.
Temperature-sensitive phenotypes are typically caused by missense mutations. The resulting amino acid substitution creates a protein that can fold into its active conformation at the lower, permissive temperature but misfolds and becomes inactive at the higher, restrictive temperature. Nonsense mutations, frameshift mutations, and promoter deletions would likely result in a non-functional product at all temperatures.
- A point mutation in the hisD gene of Salmonella renders it auxotrophic for histidine (His-). To characterize the mutation, the strain is treated with two different mutagens: hydroxylamine (which specifically induces G:C to A:T transitions) and proflavin (an intercalating agent that causes frameshifts). The His- strain shows a high rate of reversion to His+ when treated with hydroxylamine, but no increase in reversion rate with proflavin. What was the most likely original mutation in the hisD gene?
Answer: An A:T to G:C transition.
The logic of reversion analysis is key here. The strain is revertible by hydroxylamine, which causes G:C → A:T transitions. This means the reversion mutation is a change from G:C to A:T. For this to restore the wild-type function, the original mutation must have been the opposite: an A:T → G:C transition. The lack of reversion with proflavin confirms the original mutation was a base substitution, not a frameshift. Choice B is the reversion event itself, not the original mutation, a common error in interpreting these experiments.
- A strain of E. coli has a nonsense mutation in the lacZ gene, resulting in a premature UAG stop codon and an inability to metabolize lactose. A subsequent spontaneous mutation in a different gene restores the Lac+ phenotype, even though the original lacZ mutation is still present. This second mutation most likely occurred in a gene encoding:
Answer: a transfer RNA (tRNA) whose anticodon has been altered to recognize the UAG codon.
This scenario describes intergenic suppression. The second mutation compensates for the first one without correcting it. A nonsense mutation creates a premature stop codon (UAG). A mutation in a tRNA gene can alter its anticodon so that it now recognizes the stop codon and inserts an amino acid, allowing translation to continue. This is a common mechanism for nonsense suppression. Increased termination (A) would worsen the problem. Altering transcription (C) cannot fix a problem in the mRNA sequence. DNA repair (D) is ruled out because the stem states the original mutation is still present.
- A Tn5 transposon, which contains a kanamycin resistance gene and strong transcriptional terminators, inserts into the middle of the trpB gene within the polycistronic E. coli trp operon (trpE-trpD-trpC-trpB-trpA). The bacterium is grown in a rich medium containing both tryptophan and kanamycin. What is the most likely phenotype related to the trp operon genes?
Answer: The cell will produce functional TrpE, TrpD, and TrpC, but not TrpB or TrpA.
The insertion of the transposon into trpB directly disrupts the coding sequence, preventing the production of a functional TrpB protein. Because the operon is transcribed as a single polycistronic mRNA, the transcriptional terminators within the transposon will cause transcription to stop prematurely. This polar effect will prevent the transcription of any downstream genes, in this case, trpA. The upstream genes (trpE, trpD, trpC) will be transcribed normally up to the insertion point. The cell will grow because the medium supplies tryptophan.
- A new chemical compound is tested for mutagenicity using the Ames test with two different Salmonella tester strains. Strain TA100 has a missense mutation that is reverted by base substitutions. Strain TA1537 has a +1 frameshift mutation that is reverted by frameshift mutagens. The results show a high number of His+ revertant colonies for Strain TA1537, but a number of revertants close to the spontaneous background level for Strain TA100. What can be concluded about the chemical?
Answer: It is a mutagen that primarily induces frameshift mutations.
The Ames test uses different bacterial strains with specific, known mutations to diagnose the mutagenic properties of a chemical. A positive result (high number of revertant colonies) indicates that the chemical can cause mutations that reverse the original defect. In this case, the chemical caused a high rate of reversion in Strain TA1537, which is designed to detect frameshift mutagens. It did not cause a significant increase in reversions in Strain TA100, which detects base-substitution mutagens. Therefore, the most accurate conclusion is that the chemical is a mutagen that acts primarily by causing frameshift mutations.
- A strain of E. coli has a loss-of-function mutation in the mutS gene. The MutS protein is essential for initiating the mismatch repair (MMR) pathway by recognizing and binding to mispaired bases in newly synthesized DNA. This mutant strain would be expected to exhibit a higher rate of:
Answer: spontaneous point mutations, including both transitions and transversions.
The mismatch repair (MMR) system, initiated by MutS, corrects errors made by DNA polymerase during replication. These errors include base-base mismatches (which lead to substitutions) and small insertion/deletion loops. A defect in MMR leads to a 'mutator' phenotype, characterized by a dramatic increase in the rate of all types of spontaneous point mutations (transitions and transversions) as well as small frameshifts. The most general and accurate description of the consequence is an increase in spontaneous point mutations. MMR is not involved in repairing large rearrangements or UV-induced dimers.
