Molecular Biology Ultimate Cheat Sheet
1000+ words of pure high-yield concepts. Master the intricate mechanisms of Replication, Transcription, Translation, and Operon Models to guarantee your marks in the DBT BET 2026 Exam.
1. DNA Replication: The Molecular Photocopier
DNA replication is semi-conservative and always proceeds in the 5' to 3' direction. For DBT BET, the absolute highest yield area is understanding the specific enzymatic activities of prokaryotic DNA Polymerases.
The Machinery at the Replication Fork
- Helicase (DnaB in E. coli): Unwinds the double helix using ATP. It travels on the lagging strand template in the 5' → 3' direction.
- SSB Proteins: Bind to single-stranded DNA to prevent it from re-annealing and protect it from nuclease degradation.
- Primase (DnaG): An RNA polymerase that synthesizes a short RNA primer to provide a free 3'-OH group for DNA polymerase to start synthesis.
- DNA Ligase: Seals the nicks between Okazaki fragments by forming a phosphodiester bond. It requires ATP in eukaryotes and NAD+ in E. coli.
| Prokaryotic Polymerase | 3' → 5' Exonuclease (Proofreading) | 5' → 3' Exonuclease (Primer Removal) | Primary Function |
|---|---|---|---|
| DNA Pol I (Kornberg Enzyme) | Yes | Yes (Unique feature!) | Removes RNA primers and fills the gaps. Important for DNA repair. |
| DNA Pol II | Yes | No | DNA repair mechanism (SOS response). |
| DNA Pol III | Yes | No | Main replicating enzyme. Has high processivity due to the beta-clamp. |
2. Transcription & Post-Transcriptional Modifications
Transcription is the process of synthesizing RNA from a DNA template. Unlike replication, transcription does not require a primer. However, it heavily relies on promoter sequences to initiate.
Bacterial Transcription Promoters
The RNA Polymerase holoenzyme in bacteria consists of a core enzyme (α2ββ'ω) and a Sigma (σ) factor. The Sigma factor is strictly responsible for recognizing promoter regions, specifically the -10 region (Pribnow box: TATAAT) and the -35 region (TTGACA). Once transcription begins, the sigma factor dissociates.
Eukaryotic RNA Polymerases (Highly Tested)
| Eukaryotic Enzyme | Primary Product Synthesized | Sensitivity to α-Amanitin (Mushroom Toxin) |
|---|---|---|
| RNA Polymerase I | rRNA (5.8S, 18S, 28S) | Resistant |
| RNA Polymerase II | mRNA, snRNA, miRNA | Highly Sensitive (inhibits at low concentrations) |
| RNA Polymerase III | tRNA, 5S rRNA | Moderately Sensitive (inhibits at high concentrations) |
mRNA Processing in Eukaryotes
- 5' Capping: Addition of a 7-methylguanosine cap via a unique 5'-5' triphosphate linkage. Protects from RNases and helps in ribosome binding.
- Splicing: Removal of introns (non-coding) and joining of exons. Catalyzed by the Spliceosome (made of snRNPs). The intron forms a "Lariat" (loop) structure via a 2'-5' phosphodiester bond at the branch point Adenine.
- 3' Polyadenylation: Addition of ~200 Adenine residues by Poly-A Polymerase (which uniquely does not need a template). Stabilizes the mRNA.
3. Translation & Antibiotic Inhibitors
Protein synthesis translates the nucleotide sequence of an mRNA into an amino acid sequence. This is a primary target for many clinically important antibiotics, making it a favorite topic for DBT JRF examiners.
Key Translation Concepts
The charging of tRNA with its correct amino acid is done by Aminoacyl-tRNA Synthetase. This enzyme is highly accurate and uses a "Double Sieve Mechanism" for proofreading. The first amino acid in prokaryotes is fMet (N-formylmethionine), while in eukaryotes it is a normal Methionine.
In prokaryotes, the ribosome binds to the mRNA by recognizing the Shine-Dalgarno sequence located upstream of the AUG start codon. In eukaryotes, the ribosome scans for the Kozak sequence.
Antibiotics Targeting Translation (Must Memorize)
| Antibiotic | Target Domain | Mechanism of Action |
|---|---|---|
| Tetracycline | Prokaryotic 30S | Blocks the binding of aminoacyl-tRNA to the A-site. |
| Chloramphenicol | Prokaryotic 50S | Inhibits Peptidyl Transferase activity (stops peptide bond formation). |
| Streptomycin | Prokaryotic 30S | Causes misreading of the genetic code at low doses; inhibits initiation at high doses. |
| Puromycin | Both (Pro & Euk) | Structural analog of tyrosyl-tRNA. Causes premature chain termination. |
| Cycloheximide | Eukaryotic 60S | Inhibits Eukaryotic Peptidyl Transferase. (Experimental use only, not clinical) |
4. Gene Regulation: The Operon Models
The lac operon is the quintessential model of negative and positive gene regulation in bacteria. Questions often ask about the operon's state under varying sugar concentrations.
The Lac Operon (Inducible System)
It consists of structural genes (lacZ, lacY, lacA) necessary for lactose metabolism. lacZ codes for β-galactosidase, which cleaves lactose into glucose and galactose. The repressor protein (coded by lacI) binds to the operator to turn the system OFF.
Positive Control (Catabolite Repression): When glucose is absent, cAMP levels rise. cAMP binds to CAP (Catabolite Activator Protein). The CAP-cAMP complex binds near the promoter, supercharging RNA polymerase recruitment.
• High Glucose, Low Lactose: Operon OFF (Repressor bound, no CAP).
• High Glucose, High Lactose: Operon OFF/Basal (Repressor unbound, but no CAP).
• Low Glucose, High Lactose: Operon ON (Maximum Expression). cAMP is high, CAP is bound, and the Repressor is deactivated by Allolactose.
Guaranteed Exam Hits
- Wobble Hypothesis: Proposed by Francis Crick. It states that the pairing between the 3rd base of the mRNA codon and the 1st base of the tRNA anticodon is flexible (wobbly), allowing a single tRNA to recognize multiple codons (e.g., Inosine in tRNA can pair with U, C, or A).
- Rifampicin Mechanism: This antibiotic specifically binds to the beta (β) subunit of bacterial RNA Polymerase, preventing the initiation of transcription. It is widely used to treat Tuberculosis.
- Topoisomerase Inhibitors: Ciprofloxacin (a fluoroquinolone) targets bacterial DNA Gyrase (Topoisomerase II). In eukaryotic cancer therapy, Etoposide targets human Topoisomerase II, while Camptothecin targets Topoisomerase I.
- Base Excision Repair (BER): Always starts with a DNA Glycosylase enzyme, which removes a damaged base (like Uracil resulting from Cytosine deamination) to create an AP (Apurinic/Apyrimidinic) site.
- Transposons: Often called "jumping genes." Retrotransposons use a "copy and paste" mechanism via an RNA intermediate and reverse transcriptase. DNA transposons use a "cut and paste" mechanism via the Transposase enzyme.
- Histone Modification: Acetylation of histone tails (via HATs) neutralizes the positive charge of lysine, loosening chromatin (Euchromatin) and activating transcription. Deacetylation (via HDACs) represses transcription.
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