Question map
What is Cas9 protein that is often mentioned in news?
Explanation
The Cas9 enzyme acts like molecular scissors, making a double-strand cut at the specified site once the gRNA binds to the target DNA[1]. The function of Cas9 has been manipulated to precisely insert or remove specific DNA fragments from a strand of genetic material, acting as a pair of molecular scissors[2]. This makes Cas9 a crucial tool in CRISPR gene editing technology, where site-specific DNA double-strand breaks (DSBs) are induced by the Cas9 protein under the control of sg-RNA, triggering DNA repair mechanisms[3].
Option B is incorrect because while biosensors can detect DNA and pathogens, Cas9 itself is not used as a biosensor. Option C is incorrect because Cas proteins have been utilized for genome editing in plants and animals to create modified pest-resistant plants[4], but Cas9 is a protein tool used for editing, not a gene itself. Option D is incorrect because Cas9 is not a herbicidal substance; it is a protein enzyme used in the gene editing process to make precise cuts in DNA sequences.
Sources- [3] https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1133036/full
- [4] https://www.nabard.org/auth/writereaddata/tender/pub_3110250538571878.pdf
PROVENANCE & STUDY PATTERN
Guest previewThis is a classic 'Term in News' question. While static books (NCERT) explain DNA and heredity, they don't cover specific new proteins like Cas9. This question rewards the 'Newspaper Reader' over the 'Bookworm'. If a science term is in the headlines (CRISPR was massive news), you must know its one-line functional analogy.
This question can be broken into the following sub-statements. Tap a statement sentence to jump into its detailed analysis.
- Statement 1: Is Cas9 protein a molecular "scissors" used for targeted gene editing?
- Statement 2: Is Cas9 protein used as a biosensor for accurate detection of pathogens in patients?
- Statement 3: Is Cas9 a gene that makes plants pest-resistant?
- Statement 4: Is Cas9 a herbicidal substance synthesized in genetically modified crops?
- Explicitly describes Cas9 as acting "like molecular scissors" to make a double-strand cut at the targeted site.
- Connects the cut by Cas9 to targeted editing via guide RNA and cellular repair pathways that alter gene function.
- States Cas9 has been manipulated to insert or remove DNA fragments, describing it as "acting as a pair of molecular scissors."
- Frames Cas9's role directly in precision editing (inserting/removing DNA), matching the metaphor of molecular scissors for targeted editing.
- Explains that Cas9, guided by sgRNA, induces site-specific DNA double-strand breaks (DSBs).
- Shows the mechanistic basis (targeted cleavage) by which Cas9 enables gene editing, supporting the "scissors" metaphor.
Defines genetic modification as altering hereditary material (DNA) and inserting foreign genes β showing that deliberate changes to DNA underlie gene editing.
A student can combine this with the idea of a tool that makes precise DNA changes (e.g., a molecular 'scissor' that cuts DNA at chosen sites) to see why a DNA-cutting protein would be useful for targeted modification.
Explains that a gene (DNA segment) encodes proteins and that enzymes influence biological traits, linking changes in DNA to changes in cellular function.
Knowing DNA sections map to traits, a student could infer that cutting or altering a specific gene could change the encoded protein and thus the trait β suggesting a role for a precise DNA-cutting agent.
States that changing DNA information leads to different proteins and altered organisms, emphasizing that targeted DNA changes can have predictable effects.
A student can reason that a molecular mechanism that makes targeted cuts or edits in DNA would enable those predictable changes, supporting the plausibility of a 'scissors' for editing.
Describes DNA barcoding and sequencing of specific gene regions, highlighting that specific DNA sequences can be identified and targeted.
Combining sequence-identification (targeting) with a DNA-modifying tool suggests how a sequence-specific 'cutting' protein could be directed to particular genes for editing.
Explains that genes exist as discrete pieces (chromosomes) and that inheritance depends on specific DNA units, implying genes are addressable units.
A student could extend this by noting that addressable gene units make it meaningful to target and cut particular DNA loci with a molecular tool to alter inheritance or traits.
Describes laboratory diagnostic methods (virus isolation, serology) and the requirements (Biosafety level 3, specific cell-lines), highlighting that pathogen detection can rely on molecular/biological assays.
A student could note that newer molecular diagnostics aim to be faster and safer than culture-based methods and therefore investigate whether Cas9-based assays provide rapid nucleic-acid detection suitable for clinical diagnostics.
Explains DNA barcoding as sequencing short standardized gene regions to identify species, showing that sequence-based approaches are valid for accurate identification of organisms.
One could extend this by reasoning that any tool (including Cas9) that recognizes specific nucleotide sequences might be adapted as a molecular diagnostic/biosensor for pathogen detection.
Notes that diagnosis is important for managing infectious diseases and lists causes (bacteria, viruses) implying the need for accurate detection methods in clinical practice.
A student could infer that because clinical management depends on accurate diagnostics, investigating whether Cas9-based detection meets clinical accuracy requirements is a logical next step.
Mentions 'newer vaccines instruct our own body cells', indicating the existence and clinical use of recent molecular biotechnology approaches.
This suggests a pattern where modern molecular tools (beyond classical vaccines/tests) are being translated to clinical use, so one might look for Cas9 as another biotechnology repurposed for diagnostics.
Explains routes and agents of communicable diseases, emphasizing the diversity of pathogens that diagnostics must detect.
A student could use this to reason that an effective biosensor like Cas9 would need to target diverse pathogen nucleic acids and therefore check whether Cas9 systems have been adapted for multiple pathogen types.
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- States that CRISPR-associated (Cas) proteins have been used for genome editing to produce pest-resistant plants.
- Implies Cas proteins (like Cas9) are tools applied to modify plants to confer pest resistance, not themselves plant resistance genes.
- Explains CRISPR is used to target and disable genes that make plants susceptible, producing disease/pest resistance.
- Shows the role of CRISPR/Cas systems is to edit plant genes (knockouts/knock-ins) rather than being innate resistance genes themselves.
- Provides a concrete example where researchers used CRISPR-Cas9 to edit a plant gene (SlGOLS) to increase virus resistance.
- Demonstrates Cas9 functions as a genome-editing tool to create resistance by altering plant genes, not as a resistance gene itself.
Gives a definition of GMOs and states that genetic modification involves inserting a foreign gene (transgene) into a plant to confer new traits.
A student can use this rule to ask whether Cas9 is used as a transgene or as a tool for editing those transgenes to assess if it would itself be described as conferring pest resistance.
Provides a concrete example where genes from a soil bacterium were introduced into GM mustard and those genes give the plant pest-resistance.
A student could compare the biological source and function of Cas9 with the example (bacterial gene conferring resistance) to judge plausibility that Cas9 might act similarly.
Explains the general principle that genes control characteristics or traits (e.g., enzyme efficiency affects plant height).
Use this principle to recognize that for Cas9 to 'make' pest resistance it would need to encode a trait-altering product or enable changes that produce such a trait.
Mentions 'genetic engineering' as removing/replacing specific genes with information from another organism and also refers to genetic control methods for pest management.
A student could consider whether Cas9 functions as the inserted trait or as a gene-editing tool used to alter other genes implicated in pest resistance.
States that artificial selection and hybridisation can create seeds that are disease- and pest-resistant, showing multiple genetic routes to resistance.
This suggests a student should distinguish between genes that directly encode resistance and techniques (or genes) used to create resistant varieties, and then see which category Cas9 fits.
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- States CRISPR-Cas9 is used in genetically modified crops for mass commercialization, indicating Cas9-related technology appears in crop contexts.
- Describes delivery of Cas9 components (implying use as a genome-editing tool rather than a pesticide/herbicide).
- Specifically mentions 'transgenic crops expressing CRISPR/Cas9', showing crops can express Cas9.
- Context discusses editing and off-target mutations, indicating Cas9's role is genome editing rather than acting as a chemical herbicide.
- Describes Cas9 as a protein that 'selects the correct location on the host's genome' and binds to DNA, indicating a molecular editing function.
- Clarifies that the targeting sequence is separate from the Cas9 protein, supporting that Cas9 is an editing enzyme, not a herbicidal compound.
States GM crops are said to be herbicide tolerant and that GM growth is associated with use of herbicides β introduces the common trait 'herbicide tolerance' rather than that GM plants produce herbicides themselves.
A student could use this to distinguish between (A) GM plants engineered to tolerate externally applied herbicides and (B) plants engineered to synthesize a herbicidal substance, and then check whether Cas9 fits either category.
Explains that genetic modification involves inserting foreign genes (transgenes) into a plant so the plant can express new traits/proteins.
A student could reason that if Cas9 were expressed in a crop it would require a transgene encoding the Cas9 protein β then look up whether such constructs are used to make herbicides in planta.
Mentions Bt brinjal and Bt as an example where GM crops express an insecticidal protein (Bt toxin), showing GM plants can be engineered to produce pesticidal proteins.
By analogy, a student can ask whether Cas9 is used similarly as an in-plant pesticidal protein (and then compare Cas9's known function to Bt's mode of action).
Defines GM crops as plants whose DNA is modified to confer traits like resistance to bacteria, viruses and other damaging agents β showing the typical goals of modification are resistance/safety and productivity.
A student could use this to assess whether producing a herbicidal substance aligns with common GM crop objectives and then investigate Cas9's typical intended use in biotechnology.
Gives a basic definition that GM crops have DNA altered using genetic engineering techniques β framing that any novel trait (including protein synthesis) would arise from deliberate genetic changes.
A student can combine this with knowledge of what Cas9 does (a genome-editing nuclease) to judge plausibility of crops being engineered to synthesize Cas9 as a herbicide.
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- [THE VERDICT]: Sitter (Current Affairs). While the provenance score is low for static books, this was the most discussed biotech topic of the decade. Missing this means you aren't tracking S&T headlines.
- [THE CONCEPTUAL TRIGGER]: Biotechnology > Genome Editing Tools. The shift from 'Genetic Modification' (inserting foreign genes) to 'Gene Editing' (fixing existing genes).
- [THE HORIZONTAL EXPANSION]: Memorize the 'Biotech Toolbox': Zinc Finger Nucleases (ZFNs) & TALENs (Older editors), RNA Interference (Gene Silencing), CAR-T Therapy (Cancer), Mitochondrial Replacement (3-Parent Baby), and Cas12/Cas13 (Diagnostics/FELUDA).
- [THE STRATEGIC METACOGNITION]: For S&T, UPSC asks 'What is it?' and 'What does it do?'. Do not study the molecular chemical bonds. Study the metaphor: Cas9 = Scissors; Guide RNA = GPS; CRISPR = The Archive.
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A gene is a DNA segment that contains information to make a specific protein, which in turn influences traits.
High-yield for questions on heredity and biotechnology: connects the molecular basis of traits to genetic interventions and helps explain why altering DNA can change protein production. Links to topics on mutation, gene expression and phenotypic effects, enabling answers on genetic modification rationale and outcomes.
- Science , class X (NCERT 2025 ed.) > Chapter 8: Heredity > 8.2.3 How do these Traits get Expressed? > p. 131
- Science , class X (NCERT 2025 ed.) > Chapter 7: How do Organisms Reproduce? > 7.1 DO ORGANISMS CREATE EXACT COPIES OF THEMSEL THEMSELVES? > p. 113
Genetic modification involves altering an organism's DNA by inserting foreign genes to change traits.
Essential for biotechnology and agriculture segments: clarifies modern definitions of GMOs and grounds discussions of techniques used to create modified crops or organisms. Useful for policy, ethics and technology questions about gene manipulation and its applications.
- Indian Economy, Nitin Singhania .(ed 2nd 2021-22) > Chapter 9: Agriculture > GENETICALLY MODIFIED (GM) CROPS > p. 301
Chromosomes carry discrete gene units and their segregation during gamete formation preserves species DNA and transmits traits.
Central for inheritance and reproductive biology: explains mechanisms of trait transmission, foundation for understanding how targeted DNA changes in germline or somatic cells affect progeny or individual organisms. Helps answer questions on heredity, Mendelian patterns and implications of genomic edits.
- Science , class X (NCERT 2025 ed.) > Chapter 8: Heredity > separate traits, shape and colour of seeds Figure 8.5 > p. 132
- Science , class X (NCERT 2025 ed.) > Chapter 7: How do Organisms Reproduce? > 7.1 DO ORGANISMS CREATE EXACT COPIES OF THEMSEL THEMSELVES? > p. 113
Laboratory diagnosis (e.g., virus isolation, serological tests) is a primary route to confirm pathogen presence in patients.
High-yield for UPSC because questions often probe laboratory and public-health responses to outbreaks, biosafety requirements, and timelines for definitive diagnosis; links to topics on disease surveillance, public health infrastructure, and technology for detection.
- Environment and Ecology, Majid Hussain (Access publishing 3rd ed.) > Chapter 8: Natural Hazards and Disaster Management > Dengue and Chikungunya > p. 79
- Science ,Class VIII . NCERT(Revised ed 2025) > Chapter 3: Health: The Ultimate Treasure > Snapshots > p. 42
Pathogens enter and spread via routes such as airborne droplets, direct contact, and contaminated food or water, which determine testing strategies and control measures.
Core for epidemiology and health policy questions; mastering transmission modes helps in analyzing containment strategies, vaccination priorities, and prevention measures in public health scenarios.
- Science ,Class VIII . NCERT(Revised ed 2025) > Chapter 3: Health: The Ultimate Treasure > 3.4.1 How are communicable diseases caused and spread? > p. 32
- Science ,Class VIII . NCERT(Revised ed 2025) > Chapter 3: Health: The Ultimate Treasure > Snapshots > p. 42
Vaccines use weakened/dead pathogens or parts to train the immune system, and prior exposure leads to stronger subsequent immune responses.
Important for questions on immunization policy, vaccine technologies, and population immunity; connects immunology to preventive health and program implementation topics in UPSC mains and ethics-case studies.
- Science ,Class VIII . NCERT(Revised ed 2025) > Chapter 3: Health: The Ultimate Treasure > Chapter 3βββHealth: The Ultimate Treasure 45 > p. 45
- Science ,Class VIII . NCERT(Revised ed 2025) > Chapter 3: Health: The Ultimate Treasure > Ability of the body to fight diseases > p. 37
- Science ,Class VIII . NCERT(Revised ed 2025) > Chapter 3: Health: The Ultimate Treasure > Snapshots > p. 42
Plants can acquire pest-resistance through insertion of foreign genes via genetic modification.
High-yield for questions on GM crops, biotechnology policy, and biosafety; connects biotechnology with agriculture and environmental implications and enables analyses of pros/cons of transgenic crops in governance and regulation.
- Indian Economy, Nitin Singhania .(ed 2nd 2021-22) > Chapter 9: Agriculture > GENETICALLY MODIFIED (GM) CROPS > p. 301
- Environment and Ecology, Majid Hussain (Access publishing 3rd ed.) > Chapter 12: Major Crops and Cropping Patterns in India > Biotic: Living > p. 111
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Option B (Biosensor) was a prophecy. While Cas9 is the 'Scissor' for editing, its cousins Cas12 and Cas13 are now used as 'Biosensors' for detecting pathogens (e.g., the FELUDA test for COVID-19). The wrong option of today is the right question of tomorrow.
Linguistic Precision Hack: The question asks what 'Cas9 protein' is. Option C says 'A gene'. A protein is the *product* of a gene, not the gene itself. Option D says 'Herbicidal substance'βusually chemicals. Option A uses the specific, famous metaphor 'Molecular Scissors' which is the standard definition for nucleases in biology.
Link this to GS-4 (Ethics) and GS-3 (Security). Gene editing leads to 'Designer Babies' (He Jiankui case) raising ethical storms. It also links to 'Dual Use' technologies where bio-tools could be used to create bioweapons.
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