(a) Sketch out a basic transcription unit and illustrate the RNA polymerase II associated assembly of a transcription initiation complex during expression of a eukaryotic gene. 20

(b) Illustrate the steps of constructing a recombinant c-DNA from an

Question

(a) Sketch out a basic transcription unit and illustrate the RNA polymerase II associated assembly of a transcription initiation complex during expression of a eukaryotic gene. 20

(b) Illustrate the steps of constructing a recombinant c-DNA from an m-RNA. 15

(c) Explain the following :

(i) Stepwise intrinsic mechanism of apoptotic induction

(ii) Principle of DNA fingerprinting 15

UPSC Answer Check · Accepted Answer

The directive 'illustrate' demands visual representation alongside explanatory text. Structure your answer with a brief introduction on gene expression and molecular techniques, then allocate approximately 40% of content to part (a) on transcription initiation complex assembly, 30% to part (b) on cDNA construction, and 30% to part (c) covering both apoptosis mechanisms and DNA fingerprinting principles. Conclude with the significance of these techniques in biotechnology and forensic science in India.
- Part (a): Basic transcription unit showing promoter (TATA box, CAAT box), enhancer, structural gene with exons/introns, and terminator; RNA Pol II pre-initiation complex assembly with TBP, TFIID, TFIIA-H and phosphorylation of CTD heptapeptide repeats
- Part (b): cDNA synthesis steps—oligo-dT priming, reverse transcriptase action, RNase H degradation, DNA polymerase I synthesis, S1 nuclease treatment, and adapter ligation for cloning
- Part (c)(i): Intrinsic apoptotic pathway—Bcl-2 family regulation (Bax/Bak activation), mitochondrial outer membrane permeabilization, cytochrome c release, apoptosome formation with Apaf-1, caspase-9 activation, and caspase cascade execution
- Part (c)(ii): DNA fingerprinting principle—VNTR/SNP polymorphism, PCR amplification, gel electrophoresis, Southern blotting with radioactive probes, and statistical interpretation of match probability
- Molecular nomenclature accuracy: TATA-binding protein, carboxy-terminal domain, reverse transcriptase, dideoxynucleotides, caspases, restriction fragment length polymorphism
- Indian applied context: Use of DNA fingerprinting in NRC Assam, criminal investigations by CFSL Hyderabad/Kolkata, and caspase research at CCMB Hyderabad
- Comparative dimension: Contrast intrinsic vs extrinsic apoptosis briefly; distinguish genomic DNA vs cDNA applications

Dimension	Weight	Max marks	Excellent	Average	Poor
Concept correctness	22%	11	Precisely describes RNA Pol II CTD phosphorylation dynamics (Ser5 for initiation, Ser2 for elongation), correct orientation of transcription unit elements (upstream/downstream), accurate cDNA synthesis chemistry (RNA-dependent DNA polymerase activity), and correct apoptosome stoichiometry (7 Apaf-1:7 cytochrome c:7 dATP)	Generally correct but confuses RNA Pol I/II/III functions, omits CTD phosphorylation significance, or misrepresents cDNA synthesis as DNA→DNA rather than RNA→DNA	Fundamental errors such as placing enhancers downstream of promoter, confusing apoptosis with necrosis, or describing DNA fingerprinting as protein-based analysis
Diagram / labelling	24%	12	Clear hand-drawn transcription unit with labeled -35/-10 regions, TATA box at -25, Inr element, DPE; RNA Pol II PIC assembly showing TFIID→TFIIA→TFIIB→Pol II/TFIIF→TFIIE→TFIIH sequence; cDNA synthesis flowchart with enzyme labels; apoptosome wheel structure diagram	Basic diagrams present but missing critical labels (e.g., TBP in TFIID, RNase H step), poor spatial organization, or illegible handwriting affecting interpretation	Absent diagrams, or diagrams that misrepresent molecular geometry (e.g., showing DNA as single-stranded in transcription unit, omitting 5'-3' polarity)
Examples & nomenclature	18%	9	Uses specific examples: TATA-less promoters (p53, IRF genes), Moloney murine leukemia virus reverse transcriptase, caspase-3/7 as executioners, Alec Jeffreys' 1984 discovery, Indian STR loci (CSF1PO, TPOX, TH01) used by CDFD Hyderabad	Generic references to 'reverse transcriptase' without source, 'caspases' without specificity, or DNA fingerprinting without mentioning VNTR/STR distinction	Incorrect nomenclature (e.g., 'DNA transcriptase'), confused enzyme functions, or invented examples not existing in literature
Process explanation	22%	11	Stepwise logical flow for (a): PIC assembly order with TFIIH helicase/kinase activities; for (b): complete cDNA synthesis with second strand synthesis details; for (c)(i): Bcl-2 family hierarchy from BH3-only sensors to executioners; for (c)(ii): Hardy-Weinberg calculation of profile frequency	Processes described but lacking mechanistic detail (e.g., 'enzymes act' without specifying which), missing critical steps like poly-A tail requirement for cDNA, or superficial apoptosis description without MOMP regulation	Disordered sequence of events, omission of critical steps (e.g., no mention of reverse transcriptase in cDNA synthesis), or conflation of intrinsic and extrinsic pathways
Evolutionary / applied context	14%	7	Connects transcription complexity to eukaryotic gene expansion; notes retroviral origin of reverse transcriptase; discusses evolutionary conservation of apoptosis (CED genes in C. elegans); cites DNA fingerprinting in Indian legal framework (Section 45 of Indian Evidence Act, 2009 amendment) and NRC applications	Brief mention of biotechnology applications without Indian context, or generic statement about medical importance without specific linkage to question components	No applied context provided, or irrelevant digressions into unrelated molecular biology topics without connecting to the specific techniques described

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