Section 3: Genetics, Cellular and Molecular Biology
DNA replication, transcription, translation
Subtopic: Fundamentals of DNA replication, transcription, translation
Question Statement:
Determine the correctness or otherwise of the following Assertion [a] and the Reason [r]:
Assertion [a]: Ab initio gene finding algorithms that predict protein coding genes in eukaryotic genomes are not completely accurate.
Reason [r]: Eukaryotic splice sites are difficult to predict.
Options:
(A) Both [a] and [r] are false
(B) [a] is true but [r] is false
(C) Both [a] and [r] are true and [r] is the correct reason for [a]
(D) Both [a] and [r] are true but [r] is not the correct reason for [a]
GATE 2018 Biotechnology
Official Answer Key:
C
Step-by-Step Solution & Explanation
### **Official Solution & Step-by-Step Derivation (GATE BT 2018 Q.39)**
**1. Governing Concept & Question Classification**:
- **Section**: BT
- **Question Type**: **MCQ** (2 Marks)
- **Topic**: Computational Biology & Genomics (Ab Initio Gene Prediction Algorithms)
**2. Detailed Step-by-Step Analysis**:
- **Assertion [a]**: *“Ab initio gene finding algorithms that predict protein coding genes in eukaryotic genomes are not completely accurate.”*
- This assertion is **TRUE**. Unlike prokaryotes with uninterrupted open reading frames, eukaryotic genes feature complex mosaic architectures: short exons embedded within massive non-coding introns, variable 5′/3′ UTR lengths, alternative promoters, and alternative splicing isoforms. Consequently, *ab initio* algorithms (like GENSCAN, GlimmerHMM) suffer from false positive and false negative exon predictions.
- **Reason [r]**: *“Eukaryotic splice sites are difficult to predict.”*
- This reason is **TRUE**. Splice site consensus sequences (the 5′ donor GU, the 3′ acceptor AG, and the branch-point adenosine) are degenerate and short. Countless non-functional pseudo-splice sites exist throughout eukaryotic introns and intergenic regions that match the consensus degenerate motif just as closely as real splice sites. This high degeneracy makes accurate splice site prediction extraordinarily challenging.
- Furthermore, because splice site prediction is a primary bottleneck causing mispredicted exon-intron boundaries in eukaryotic *ab initio* modeling, **Reason [r] is the direct correct causal reason for Assertion [a]**.
- **Option-by-Option Evaluation**:
- **Option (A) [INCORRECT]**: Both statements are well-established facts.
- **Option (B) [INCORRECT]**: [r] is true.
- **Option (C) [CORRECT]**: Both [a] and [r] are true, and [r] is the correct explanatory reason for [a].
- **Option (D) [INCORRECT]**: [r] directly explains why *ab initio* eukaryotic gene predictions lack complete accuracy.
**3. Final Answer / Verification Summary**:
- **Official GATE Answer Key**: **C**
- **Scoring Criteria**: +2.0 Marks (Negative marking: -0.67 marks).
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