Virus Structure and Classification (2B) - Bio & Biochem

1. Virus JJ is an RNA virus that is detergent-sensitive. In an entry assay, antibodies against a viral surface protein block attachment, while antibodies against an internal capsid protein do not. When virions are stripped of envelope proteins (but not the lipid bilayer) using a mild protease, they bind cells poorly. Based on the passage, how does the structure influence pathogenicity?
   Answer: Envelope-associated surface proteins mediate attachment; loss of these proteins reduces binding and infection This question tests understanding of virus structure and classification, specifically how enveloped viruses utilize surface proteins for host cell attachment. Viruses are classified based on genome type, presence of an envelope, and structural components, with enveloped viruses featuring a lipid bilayer derived from the host cell that is sensitive to detergents and often studded with viral glycoproteins essential for infection. The passage describes Virus JJ as a detergent-sensitive RNA virus, indicating it is enveloped, and provides data on antibody blocking and protease treatment affecting attachment. The correct answer, A, follows from the data because antibodies against surface proteins block attachment and protease removal of envelope proteins reduces binding, demonstrating these proteins mediate host cell interaction and thus pathogenicity through infection efficiency. A common distractor like B fails due to the misconception that internal capsid proteins, rather than exposed envelope glycoproteins, are primarily responsible for attachment, ignoring that capsid proteins are shielded in enveloped viruses. To verify similar questions, always cross-reference experimental outcomes, such as sensitivity to treatments, with structural features like envelope presence. A useful strategy is to eliminate choices contradicting data, ensuring the explanation aligns with observed effects on viral entry.
2. A virus isolated from blood is sensitive to chloroform and shows a helical nucleocapsid by EM. When infected cells are treated with actinomycin D (inhibits cellular DNA-dependent RNA polymerase II), viral mRNA production is unaffected. However, when cells are treated with a small-molecule inhibitor of viral RNA-dependent RNA polymerase, viral mRNA is abolished. Which classification best fits the virus described?
   Answer: Enveloped RNA virus requiring an RNA-dependent RNA polymerase The skill being tested is virus classification via inhibitor responses and structural features for MCAT biological foundations. Viruses are classified by genome (requiring specific polymerases) and envelope (conferring chloroform sensitivity and helical nucleocapsids). The virus is chloroform-sensitive with helical nucleocapsid, unaffected by actinomycin D but blocked by RdRp inhibitor, indicating RNA genome independent of host transcription. Answer A fits as enveloped RNA viruses like paramyxoviruses use viral RdRp for mRNA, matching inhibitor data. Distractor B errs by suggesting host RNA pol II dependence, ignoring actinomycin D insensitivity, a misconception for DNA viruses. Confirm by assaying polymerase inhibitors' effects on replication. Reason by excluding classifications mismatched with structural (EM) and functional (inhibitor) evidence.
3. Two viruses (A and B) infect the same mammalian cell line. Virus A infectivity decreases to 5% after chloroform treatment; Virus B infectivity is unchanged. When antibodies against a known host cell receptor are added, Virus A entry is blocked, but Virus B entry is unaffected. Inhibiting endosomal acidification strongly reduces Virus A infection but has minimal effect on Virus B. Based on the passage, how does structural organization most likely influence the entry mechanism of Virus A compared with Virus B?
   Answer: Virus A likely uses envelope glycoproteins for receptor-mediated endocytosis and fusion triggered by low pH This question tests understanding of how virus structure determines entry mechanisms. Virus entry mechanisms are fundamentally linked to structural organization: enveloped viruses typically use membrane fusion, while non-enveloped viruses use other mechanisms. The passage shows Virus A is chloroform-sensitive (enveloped), uses receptor-mediated entry (antibody blockade), and requires endosomal acidification (pH-dependent fusion). This profile matches enveloped viruses that bind receptors via envelope glycoproteins, undergo endocytosis, and fuse when endosomal pH drops. Choice A correctly describes this mechanism. Choice B incorrectly suggests tail apparatus (bacteriophage feature), choice C reverses the envelope assignments contradicting chloroform data, and choice D incorrectly claims receptor-independent entry despite antibody blocking data. The principle: enveloped viruses often use pH-triggered fusion after receptor-mediated endocytosis, while non-enveloped viruses may use direct penetration or other pH-independent mechanisms.
4. Virus HH is characterized by nuclease sensitivity assays. After capsid disruption, its genome is degraded by DNase but not RNase. Transfection of purified genome into cells results in viral protein expression only when a promoter recognized by host RNA polymerase II is present on the introduced DNA. Infectivity is reduced by detergents. Which classification best fits the virus described?
   Answer: Enveloped DNA virus that uses host transcription machinery The skill being tested is classifying by genome and transcription for MCAT. DNA viruses use host pol II if promoters match, may be enveloped. Virus HH genome DNase-sensitive post-disruption, transfection requires pol II promoter, detergent-labile. Answer D fits as enveloped DNA like poxviruses use host transcription. Distractor B errs for non-enveloped +RNA, ignoring DNase and promoter data. Check transfection with/without promoters. Reason by matching nuclease and dependence.
5. An unknown virus (Virus R) is suspected to be a retrovirus. In infected cells, viral RNA is detected early, followed by a stable DNA form that persists even after viral entry inhibitors are removed. A reverse transcriptase inhibitor markedly reduces production of new infectious particles. Purified virions lose infectivity after detergent treatment. Which classification best fits Virus R?
   Answer: Enveloped single-stranded RNA virus that replicates through a DNA intermediate using reverse transcriptase This question tests retrovirus classification based on replication strategy. Retroviruses are uniquely defined by their RNA genome, reverse transcription to DNA, and envelope structure. The passage provides classic retroviral markers: early viral RNA followed by stable DNA form (reverse transcription), reverse transcriptase inhibitor sensitivity (confirming RT dependence), and detergent sensitivity (enveloped). These features definitively identify a retrovirus that packages RNA, reverse transcribes to DNA for integration, and buds with an envelope. Choice A correctly identifies all retroviral features. Choice B incorrectly suggests DNA genome contradicting RNA detection, choice C incorrectly identifies dsRNA genome, and choice D incorrectly suggests host polymerase mediates reverse transcription rather than viral RT. The diagnostic principle: only retroviruses combine RNA genome, reverse transcription to DNA intermediate, and enveloped structure - this unique replication strategy distinguishes them from all other virus families.
6. A newly identified Virus Y was examined for genome type using nuclease protection assays. Intact virions were resistant to both DNase I and RNase A. After capsid disruption, the extracted genome was degraded by RNase A but not by DNase I. When infected cells were treated with a drug that inhibits RNA-dependent RNA polymerase (RdRp), production of new virions decreased by 95%. Based on these results, which classification best fits Virus Y?
   Answer: RNA virus that depends on an RdRp during replication This question tests the ability to determine viral genome type through nuclease protection assays and replication inhibitor studies. Virus classification fundamentally distinguishes RNA viruses from DNA viruses based on genome composition and replication strategy. The intact virion's resistance to both nucleases indicates the genome is protected within the capsid, while post-disruption RNase sensitivity (but not DNase sensitivity) definitively identifies an RNA genome. The 95% reduction with RdRp inhibitor confirms this RNA virus uses RNA-dependent RNA polymerase for replication, a hallmark of RNA viruses. Choice B incorrectly suggests a DNA virus, contradicting the RNase sensitivity data. Choice C describes a retrovirus scenario not supported by the data. A key principle is that RNA viruses must encode their own RNA polymerase since host cells lack the machinery to replicate RNA genomes.
7. An unknown virus is isolated from a hospital outbreak. The genome is RNA. In purified virions, a viral RNA-dependent RNA polymerase activity is detected. When the genome is directly transfected into cells, no infectious particles are produced unless the polymerase protein is co-delivered. Which classification best fits the virus described?
   Answer: Negative-sense single-stranded RNA virus The skill being tested is distinguishing RNA virus senses by enzyme requirements in MCAT classification. Negative-sense ssRNA viruses package RdRp for initial transcription, unlike positive-sense using host machinery directly. Virus has RNA genome with RdRp activity in virions, requiring co-delivery for infectivity upon transfection. Answer D is correct as -ssRNA needs polymerase for mRNA, matching transfection failure without it. Distractor B fails for +ssRNA, autonomous in translation, misconstruing enzyme need. Verify by co-transfecting enzymes with genome. Strategize by testing naked genome infectivity.
8. Two viral isolates were compared in the same cell line. Virus A produced infectious particles even when cells were treated with brefeldin A (blocks ER-to-Golgi trafficking), but infectivity dropped by 0.2 log10 after 30 minutes in 0.1% bile salts. Virus B lost 4.0 log10 infectivity after 30 minutes in 0.1% bile salts and produced markedly fewer infectious particles when cells were treated with brefeldin A. Both viruses were resistant to protease when intact but became protease-sensitive after detergent treatment. Which conclusion about structural classification is best supported by the data?
   Answer: Virus A is non-enveloped and Virus B is enveloped, consistent with bile-salt sensitivity and secretory-pathway dependence This question tests understanding of how viral structure determines environmental stability and cellular trafficking requirements. Virus classification distinguishes enveloped viruses (with lipid bilayers acquired through cellular membranes) from non-enveloped viruses (protein capsids only). The data shows Virus A resists bile salts (detergents that disrupt lipid membranes) and doesn't require the secretory pathway (brefeldin A has no effect), indicating a non-enveloped structure. Virus B is bile-salt sensitive and requires ER-to-Golgi trafficking for assembly, indicating an enveloped virus that acquires its membrane through the secretory pathway. Choice A incorrectly states bile salts disrupt protein capsids when they actually target lipid membranes. The protease resistance of intact virions for both viruses confirms structural integrity, while detergent-induced protease sensitivity shows both have protein components normally protected. A reliable check is that enveloped viruses are typically more sensitive to environmental stresses like bile salts.
9. Virus CC is an RNA virus. In infected cells, viral mRNA appears only after a delay, and purified virions contain an enzyme that synthesizes RNA from an RNA template. When purified genomic RNA is transfected into cells, no viral proteins are detected. Which classification best fits the virus described?
   Answer: Negative-sense single-stranded RNA virus The skill being tested is classifying RNA viruses by replication timing and enzymes for MCAT. Negative-sense ssRNA viruses delay mRNA via RdRp-dependent transcription, unlike immediate positive-sense. Virus CC has delayed mRNA, virion RdRp, transfection failure, indicating -ssRNA. Answer A fits as RdRp synthesizes mRNA from template, explaining delay and transfection. Distractor B errs for +ssRNA, directly translatable, misconstruing delay. Check mRNA kinetics and transfection. Reason by evaluating enzyme packaging and genome functionality.
10. Virus T is resistant to detergent but loses infectivity after exposure to 60°C for 10 min. EM shows an icosahedral capsid with no visible membrane. Infected cells produce viral proteins even when treated with brefeldin A (blocks ER-to-Golgi trafficking), but virion release into supernatant is reduced. Which classification best fits the virus described?
    Answer: Non-enveloped virus; assembly may be independent of secretory trafficking, but release can still be affected by membrane pathways The skill being tested is classifying viruses by envelope and assembly pathways for MCAT. Non-enveloped viruses have detergent-resistant capsids, assemble cytoplasmically, but may use membrane pathways for release without acquiring envelopes. Virus T is detergent-resistant, heat-labile, icosahedral without membrane, with brefeldin A reducing release but not protein production. Answer A fits as non-enveloped viruses like adenoviruses can use secretory paths for egress, matching data. Distractor B misconstrues detergent resistance as envelope robustness, ignoring EM evidence. Check inhibitor effects on assembly vs release. Reason by integrating structural (EM) and functional (inhibitor) data.
11. Investigators compare two purified viruses for genome type. After capsid disruption, nucleic acid from Virus U is degraded by DNase I but not RNase A; nucleic acid from Virus V is degraded by RNase A but not DNase I. In cells, Virus U replication is inhibited by a drug that blocks DNA polymerase, while Virus V replication is inhibited by an RdRP inhibitor. Which pairing of classifications best fits Viruses U and V, respectively?
    Answer: U: double-stranded DNA virus; V: RNA virus requiring RdRP This question tests genome classification through nuclease sensitivity and polymerase requirements. Virus classification fundamentally distinguishes DNA from RNA genomes through differential nuclease sensitivity after capsid disruption. The passage shows Virus U genome is DNase-sensitive (DNA) and requires DNA polymerase, while Virus V genome is RNase-sensitive (RNA) and requires RdRP. This clearly identifies U as a DNA virus and V as an RNA virus. Choice B correctly identifies U as double-stranded DNA virus (though single vs double-stranded isn't definitively shown) and V as RNA virus requiring RdRP. Choice A incompletely specifies the classifications, choice C incorrectly identifies U as retrovirus despite DNA genome, and choice D incorrectly identifies both as non-viral agents. The fundamental principle: after capsid disruption, DNA genomes are specifically degraded by DNase while RNA genomes are degraded by RNase - this simple test definitively distinguishes genome type.
12. A virus isolated from seawater infects bacteria. EM reveals an icosahedral head with a long tail and tail fibers. The particle is resistant to detergents, and infectivity is lost after DNase treatment only when the capsid is mechanically disrupted. Which classification best fits the virus described?
    Answer: Bacteriophage with a DNA genome packaged in a head-tail structure The skill being tested is classifying bacteriophages by structure and genome protection for MCAT. Phages often have head-tail structures with DNA genomes, detergent-resistant due to lack of envelope. The virus infects bacteria, has head-tail EM, detergent-resistant, DNase-sensitive only post-disruption. Answer D is correct as this matches tailed DNA phages like T4, with capsid protecting genome. Distractor B fails for enveloped RNA, ignoring bacterial host and resistance, a host misconception. Verify by host specificity and nuclease assays. Strategize by combining EM with functional tests.
13. An experiment aims to classify Virus BB as enveloped vs non-enveloped. Researchers treat virions with either (i) detergent, (ii) protease, or (iii) RNase, then measure infectivity. Detergent reduces infectivity by 10,000-fold; protease reduces infectivity by 100-fold; RNase has no effect unless detergent is applied first. Which classification best fits the virus described?
    Answer: Enveloped virus with a protein capsid protecting its genome The skill being tested is using treatment assays to classify virus structure for MCAT. Enveloped viruses protect genomes via lipid and capsid, detergent exposes to enzymes, protease targets surface proteins. Detergent greatly reduces infectivity, protease moderately, RNase only post-detergent, indicating envelope and internal capsid. Answer D is correct as this pattern shows envelope-mediated protection with protein involvement. Distractor B fails by suggesting exposed genome, ignoring RNase resistance intact, a protection misconception. Verify by sequential treatments. Strategize by assessing enzyme access pre/post-disruption.
14. Virus DD is tested for entry pathway. Fusion inhibitors that block low-pH-triggered conformational changes prevent infection. Detergent treatment abolishes infectivity. However, raising endosomal pH blocks infection only when applied during the first 30 minutes post-inoculation. Based on the passage, how does the structure influence pathogenicity?
    Answer: An envelope fusion protein likely requires endosomal acidification to mediate membrane fusion during early entry The skill being tested is how structure dictates entry pathways in pathogenicity for MCAT. Enveloped viruses often require low-pH endosomal fusion via glycoproteins, detergent-sensitive. Virus DD is blocked by fusion inhibitors and endosomal pH raise early, detergent-labile. Answer C is correct as envelope proteins need acidification for fusion, influencing entry and pathogenicity. Distractor B misconstrues as non-enveloped neutral fusion, ignoring detergent and pH data. Check timing of inhibitors. Reason by correlating inhibitors with entry stages.
15. Virus M and Virus N were each incubated with neutralizing antibody, then added to cells. For Virus M, antibody prevented attachment but had little effect if added 10 minutes after infection began. For Virus N, antibody still reduced infection when added 30 minutes after infection began. Virus N infectivity was decreased by chloroform extraction, while Virus M infectivity was unchanged by chloroform. Which interpretation best fits these findings?
    Answer: Virus N is enveloped and may require prolonged extracellular or surface-associated steps, allowing later neutralization This question tests understanding of how viral structure influences neutralization kinetics and entry mechanisms. Virus classification reveals that enveloped viruses often have extended, multi-step entry processes compared to non-enveloped viruses. The data shows Virus N remains neutralizable 30 minutes post-infection and is chloroform-sensitive (indicating an envelope), while Virus M has rapid, irreversible entry and chloroform resistance (indicating non-enveloped). Extended neutralization windows suggest prolonged surface interactions or slow fusion processes typical of some enveloped viruses. Choice B incorrectly claims antibodies dissolve lipid envelopes when they actually block protein functions. Choice C contradicts the chloroform data showing differential sensitivity. The key insight is that structural differences create distinct temporal windows for antibody intervention.
16. Virus AA is purified and analyzed. The genome is DNA. Early viral mRNA synthesis is blocked by actinomycin D. EM shows an icosahedral capsid and a surrounding lipid membrane. Infectivity is reduced by detergents. Which classification best fits the virus described?
    Answer: Enveloped DNA virus that relies on host DNA-dependent RNA polymerase for transcription The skill being tested is classifying viruses by genome and transcription dependence for MCAT. DNA viruses often use host RNA pol II for mRNA, blocked by actinomycin D, and may be enveloped (detergent-sensitive). Virus AA has DNA genome, actinomycin D blocks mRNA, icosahedral with membrane, detergent-labile. Answer A fits as enveloped DNA viruses like herpesviruses rely on host transcription. Distractor B misconstrues as non-enveloped RNA with own polymerase, ignoring actinomycin sensitivity. Check inhibitor effects on transcription. Reason by matching genome type to polymerase dependence.
17. An unknown virus was tested for how it initiates infection. Binding to host cells was reduced 90% by pre-incubating the virus with a monoclonal antibody against a viral surface glycoprotein. Treating virions with a glycosidase that removes N-linked glycans reduced infectivity by 80% but did not disrupt the capsid. Chloroform extraction reduced infectivity by 4 log10. Based on the passage, how does the structure influence pathogenicity?
    Answer: Envelope glycoproteins (and their glycans) mediate attachment/entry, so disrupting the envelope or glycosylation reduces infectivity This question tests understanding of how viral envelope glycoproteins mediate pathogenicity through attachment and entry. Virus classification recognizes that enveloped viruses use glycoproteins embedded in their lipid bilayer for host cell recognition and entry. The data shows antibody blocks a surface glycoprotein reducing binding, glycosidase treatment (removing sugar modifications) reduces infectivity, and chloroform (disrupting lipids) destroys infectivity - all pointing to an enveloped virus whose glycoproteins are critical for infection. The glycan modifications on these proteins often determine tissue tropism and immune evasion. Choice A incorrectly describes a non-enveloped virus and misinterprets glycosidase effects. Choice C mentions peptidoglycan, a bacterial component not found in viruses. The key insight is that envelope glycoproteins and their post-translational modifications are primary determinants of viral pathogenicity.
18. To determine whether Virus S is enveloped, researchers split a viral stock into two aliquots. Aliquot 1 is treated with 1% ether; Aliquot 2 is untreated. Both are then used to infect cells, and viral RNA copies in supernatant are measured 24 h later by qRT-PCR. Ether-treated samples show a 1000-fold decrease in RNA copies relative to untreated. What is most likely the method of classification for this virus?
    Answer: Classify as enveloped based on lipid-solvent sensitivity reducing infectivity/replication The skill being tested is methods for classifying viruses by envelope using stability assays in MCAT. Envelope classification uses lipid solvents like ether, which disrupt membranes and reduce infectivity in enveloped viruses. Ether treatment decreases Virus S RNA copies 1000-fold, indicating envelope disruption impairs replication. Answer D is correct as solvent sensitivity confirms enveloped status via infectivity/replication loss. Distractor B errs by linking ether to DNA disruption, misconstruing solvent effects on lipids not nucleic acids. Confirm with qRT-PCR post-treatment for replication impact. Strategize by comparing treated vs untreated infectivity metrics.
19. Virus EE is resistant to ether and chloroform. EM shows a naked icosahedral particle. In a simulated gastric fluid assay (pH 2.0 with pepsin), 70% of infectivity remains after 30 min. In contrast, a control enveloped virus loses >99.9% infectivity. Which classification best fits the virus described?
    Answer: Non-enveloped virus with a stable capsid suited for fecal–oral transmission The skill being tested is classifying viruses by stability for transmission routes in MCAT. Non-enveloped viruses resist solvents and acid, suited for fecal-oral spread. Virus EE is ether/chloroform-resistant, icosahedral naked, retains infectivity in gastric fluid unlike enveloped control. Answer D fits as non-enveloped like noroviruses are stable for GI transmission. Distractor B errs by claiming detergent-resistant envelope, ignoring EM naked particle. Verify with stability assays. Strategize by comparing to known virus behaviors in environments.
20. A researcher suspects a virus is enveloped. In a pilot study, infectivity is reduced by 99% after 5 minutes with 0.1% Triton X-100, but infectivity is unchanged after exposure to trypsin when virions are intact. When Triton X-100 and trypsin are applied together, infectivity drops below the limit of detection. Which classification best fits the virus described?
    Answer: Enveloped virus with detergent-sensitive lipid membrane that shields protein components from protease until disrupted This question tests the ability to interpret protease protection assays in virus classification. Virus classification uses the principle that enveloped viruses have lipid membranes shielding internal proteins from proteases until the membrane is disrupted. The data shows Triton X-100 (a detergent) reduces infectivity alone, indicating membrane dependence, while trypsin only works after detergent treatment, confirming proteins are normally protected by the envelope. This pattern is diagnostic for enveloped viruses. Choice B incorrectly describes non-enveloped viruses as having polysaccharide capsules, a bacterial feature. Choice D misinterprets the data by claiming cellular rather than viral effects. The key strategy is recognizing that sequential treatment (detergent then protease) specifically tests for envelope-mediated protection of viral proteins.

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