📝 Transcription & Genetic Code
Learn transcription and genetic code properties for CUET Agriculture. Central dogma, RNA polymerase, promoter regions and wobble hypothesis.
Central Dogma of Molecular Biology
Proposed by Francis Crick (1958). The flow of genetic information follows a specific direction:
DNA → (Transcription) → RNA → (Translation) → Protein
Exceptions to the central dogma:
- Reverse transcription: RNA → DNA (by reverse transcriptase in retroviruses, e.g., HIV). Discovered by Howard Temin and David Baltimore — Nobel Prize 1975.
- RNA replication: RNA → RNA (RNA viruses, e.g., influenza, SARS-CoV-2 — by RNA-dependent RNA polymerase).
- Prions: Protein → Protein (infectious proteins, no nucleic acid; cause mad cow disease/BSE).
Types of RNA
| Type | Full Name | % of Total RNA | Function |
|---|---|---|---|
| rRNA | Ribosomal RNA | ~80% | Structural component of ribosomes; catalytic (ribozyme) in peptide bond formation |
| tRNA | Transfer RNA | ~15% | Carries amino acids to ribosome; adaptor molecule |
| mRNA | Messenger RNA | ~3-5% | Carries genetic code from DNA to ribosome; template for protein synthesis |
TIP
Despite being most discussed, mRNA is the least abundant (~3-5%). rRNA dominates at 80% because ribosomes are needed in enormous quantities.
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Central Dogma of Molecular Biology
Proposed by Francis Crick (1958). The flow of genetic information follows a specific direction:
DNA → (Transcription) → RNA → (Translation) → Protein
Exceptions to the central dogma:
- Reverse transcription: RNA → DNA (by reverse transcriptase in retroviruses, e.g., HIV). Discovered by Howard Temin and David Baltimore — Nobel Prize 1975.
- RNA replication: RNA → RNA (RNA viruses, e.g., influenza, SARS-CoV-2 — by RNA-dependent RNA polymerase).
- Prions: Protein → Protein (infectious proteins, no nucleic acid; cause mad cow disease/BSE).
Types of RNA
| Type | Full Name | % of Total RNA | Function |
|---|---|---|---|
| rRNA | Ribosomal RNA | ~80% | Structural component of ribosomes; catalytic (ribozyme) in peptide bond formation |
| tRNA | Transfer RNA | ~15% | Carries amino acids to ribosome; adaptor molecule |
| mRNA | Messenger RNA | ~3-5% | Carries genetic code from DNA to ribosome; template for protein synthesis |
TIP
Despite being most discussed, mRNA is the least abundant (~3-5%). rRNA dominates at 80% because ribosomes are needed in enormous quantities.
tRNA Structure (Cloverleaf Model)
- Described by Robert Holley (1965) — first nucleic acid to be fully sequenced (yeast alanine-tRNA). Nobel Prize 1968.
- L-shaped 3D structure; Cloverleaf shape in 2D.
- ~75-90 nucleotides long.
Key features:
- Acceptor arm (CCA arm) — 3' end sequence CCA; amino acid binds here. Universal across all tRNAs.
- Anticodon arm — contains the anticodon (3 bases complementary to mRNA codon).
- D arm (DHU arm) — contains dihydrouridine; recognition site for aminoacyl-tRNA synthetase.
- TψC arm — contains ribothymidine and pseudouridine (ψ); helps ribosome binding.
- Variable arm — varies in size; used for tRNA classification.
NOTE
tRNA has several unusual/modified bases: pseudouridine (ψ), dihydrouridine (D), inosine (I). These are important for tRNA stability and function.
Transcription (DNA → RNA)
Transcription copies genetic information from one strand of DNA into an RNA molecule.
- Catalyzed by RNA polymerase.
- Occurs in the 5'→3' direction.
- No primer needed (unlike DNA replication).
Key Terms
| Term | Definition |
|---|---|
| Template strand (Antisense) | DNA strand read by RNA polymerase (3'→5'); complementary to mRNA |
| Coding strand (Sense/Non-template) | Same sequence as mRNA (with T instead of U); NOT read by RNA polymerase |
| Promoter | DNA sequence where RNA polymerase binds to initiate transcription |
| Terminator | DNA sequence signaling end of transcription |
| Transcription unit | Promoter + Structural gene + Terminator |
Transcription in Prokaryotes
RNA Polymerase in E. coli
- Single type of RNA polymerase synthesizes all RNA types (mRNA, tRNA, rRNA).
- Holoenzyme = Core enzyme + Sigma (σ) factor.
- Core enzyme: α₂ββ'ω
- σ factor: Required for promoter recognition; most common = σ⁷⁰.
- After initiation, sigma factor dissociates → core enzyme continues elongation alone.
Steps of Prokaryotic Transcription
1. Initiation:
- RNA polymerase holoenzyme binds to the promoter.
- Pribnow box (-10 region): consensus TATAAT; DNA unwinds here (A-T pairs = 2 H-bonds, easier to separate).
- -35 region: consensus TTGACA; first contact point of RNA polymerase.
- +1 site: Transcription start; first nucleotide usually a purine (A or G).
- DNA unwinds locally (~17 bp) → transcription bubble / open complex.
2. Elongation:
- Sigma factor released after ~8-10 nucleotides.
- Core enzyme moves along template strand 3'→5'.
- RNA synthesized 5'→3' (NTPs: ATP, UTP, GTP, CTP).
- Speed: ~40-50 nucleotides/second in prokaryotes.
3. Termination:
Two termination mechanisms
**Rho-independent (Intrinsic):** Terminator sequence forms a **GC-rich hairpin (stem-loop)** followed by a run of **U's** in the mRNA. Hairpin causes polymerase to pause; weak rU-dA bonds break → RNA releases.Rho-dependent: Rho protein (ρ) — a helicase that moves along mRNA 5'→3'. When RNA polymerase pauses at the terminator, rho catches up and unwinds the RNA-DNA hybrid → RNA released.
Transcription in Eukaryotes
Three RNA Polymerases
| RNA Polymerase | Location | Product | Sensitivity to α-amanitin |
|---|---|---|---|
| RNA Pol I | Nucleolus | rRNA (28S, 18S, 5.8S) | Insensitive |
| RNA Pol II | Nucleoplasm | mRNA (and snRNA) | Most sensitive |
| RNA Pol III | Nucleoplasm | tRNA, 5S rRNA, snRNA | Moderately sensitive |
WARNING
α-amanitin — toxin from Amanita phalloides (death cap mushroom); inhibits RNA Pol II most strongly. Stops mRNA production → protein synthesis halts → organ failure.
Eukaryotic Promoter Elements
- TATA box (Hogness box) — TATAAA at -25 to -30. Analogous to prokaryotic Pribnow box.
- CAAT box — at -70 to -80; determines frequency of initiation.
- GC box — at -110; associated with housekeeping genes.
- Enhancers — can be thousands of bp upstream or downstream; increase transcription rate.
- Transcription factors (TFs) — proteins helping RNA Pol II bind promoter (e.g., TFIID binds TATA box via TBP).
Post-Transcriptional Modifications (RNA Processing)
In eukaryotes, the primary transcript (hnRNA — heterogeneous nuclear RNA / pre-mRNA) undergoes modifications before becoming mature mRNA. Prokaryotic mRNA has NO such modifications — it is translated even while being transcribed (coupled transcription-translation).
1. 5' Capping
- Addition of 7-methylguanosine (m⁷G) cap to the 5' end via a 5'-5' triphosphate linkage.
- Functions: Protects mRNA from degradation; ribosome recognition; aids nuclear export.
2. 3' Polyadenylation (Poly-A Tail)
- Addition of 100-250 adenine nucleotides (poly-A tail) by poly-A polymerase.
- Signal: AAUAAA sequence (polyadenylation signal).
- Functions: Protects from degradation; mRNA export; translation efficiency; stability.
3. RNA Splicing
- Removal of introns (non-coding/intervening sequences) and joining of exons (expressed/coding sequences).
- Carried out by the spliceosome — complex of snRNPs and proteins.
- snRNAs: U1, U2, U4, U5, U6 — recognize splice sites.
- Lariat structure — branched intermediate formed during splicing.
- Splice site sequences: 5' splice site = GU; 3' splice site = AG.
- GT-AG rule (DNA level: GU-AG at RNA level) — introns begin with GU and end with AG.
Split Genes (Interrupted Genes)
- Discovered by Richard Roberts and Phillip Sharp (1977) — Nobel Prize 1993.
- Eukaryotic genes have exons interspersed with introns.
- Prokaryotic genes are generally continuous (no introns).
Alternative Splicing
- One gene → multiple mRNAs (and thus multiple proteins) by including/excluding different exons.
- Example: Drosophila Dscam gene → over 38,000 different mRNAs.
- Explains how ~20,000 human genes encode >100,000 different proteins.
Genetic Code
Properties
The genetic code was deciphered by Marshall Nirenberg, Har Gobind Khorana, and Robert Holley — Nobel Prize 1968.
| Property | Description |
|---|---|
| Triplet | Each codon = 3 consecutive nucleotides → one amino acid |
| Non-overlapping | Codons read sequentially without sharing nucleotides |
| Commaless (Continuous) | No gaps or punctuation between codons |
| Non-ambiguous | Each codon codes for only one amino acid |
| Degenerate (Redundant) | Multiple codons can code for the same amino acid (e.g., 6 codons for Leu/Ser/Arg) |
| Universal | Same code in almost all organisms (few exceptions in mitochondria) |
| Unidirectional | Read in 5'→3' direction on mRNA |
NOTE
Non-ambiguous ≠ Degenerate. Non-ambiguous = one codon → one amino acid. Degenerate = one amino acid ← multiple codons. These coexist.
Special Codons
| Codon | Function |
|---|---|
| AUG | Start codon (codes for Methionine; in prokaryotes = N-formyl methionine fMet) |
| UAA | Stop codon — "Ochre" |
| UAG | Stop codon — "Amber" |
| UGA | Stop codon — "Opal/Umber" |
- 64 codons total (4³ = 64).
- 61 sense codons for 20 amino acids.
- 3 stop (nonsense) codons.
- Methionine (AUG) and Tryptophan (UGG) — coded by only one codon each (non-degenerate).
Wobble Hypothesis
- Proposed by Francis Crick (1966).
- The 3rd position of the codon and 1st position of the anticodon can form non-standard (wobble) base pairs.
- Allows a single tRNA to recognize more than one codon (explains degeneracy with fewer than 61 tRNAs).
- Wobble pairs: G-U, I-U, I-C, I-A (I = inosine).
Key Points to Remember
- Central dogma: DNA → RNA → Protein (Crick, 1958); exceptions: reverse transcription (HIV), RNA replication (RNA viruses), prions
- tRNA: cloverleaf model (Holley, 1965; Nobel 1968); 3' end = CCA; anticodon loop recognizes codon
- Prokaryotes: one RNA polymerase; σ⁷⁰ for promoter recognition; Pribnow box (TATAAT, -10), -35 region (TTGACA)
- Eukaryotes: 3 RNA polymerases; RNA Pol II → mRNA; TATA box (-25 to -30); α-amanitin inhibits RNA Pol II most
- RNA processing: 5' m⁷G cap, poly-A tail (100-250 A's, signal AAUAAA), splicing (spliceosome, GT-AG rule)
- Split genes: Roberts & Sharp (1977), Nobel 1993; exons = expressed, introns = intervening
- Genetic code: 64 codons, 61 sense + 3 stop (UAA/UAG/UGA); AUG = start; degeneracy; universal; wobble (Crick, 1966)
- Met (AUG) and Trp (UGG) = only amino acids with single codon
Summary Cheat Sheet
| Concept / Topic | Key Details / Explanation |
|---|---|
| Central Dogma | DNA → RNA → Protein; proposed by Francis Crick (1958) |
| Exceptions to central dogma | Reverse transcription (RNA → DNA; retroviruses/HIV; Temin & Baltimore, Nobel 1975) RNA replication (RNA → RNA; RNA viruses) Prions (Protein → Protein; no nucleic acid) |
| rRNA | ~80% of total RNA; structural/catalytic component of ribosomes |
| tRNA | ~15%; carries amino acids; adaptor molecule |
| mRNA | ~3-5% (least abundant); template for protein synthesis |
| tRNA structure | Cloverleaf (2D) / L-shaped (3D); described by Robert Holley (1965), Nobel 1968; ~75-90 nucleotides |
| tRNA key features | CCA at 3' end (amino acid attachment) Anticodon arm (recognizes mRNA codon) D arm (dihydrouridine) TψC arm (ribosome binding) |
| Template strand | Antisense; read by RNA polymerase 3'→5' |
| Coding strand | Sense; same sequence as mRNA (T instead of U); NOT read by polymerase |
| Transcription unit | Promoter + Structural gene + Terminator |
| Prokaryotic RNA polymerase | Single type; holoenzyme = core (α₂ββ'ω) + σ factor (σ⁷⁰ most common) |
| Pribnow box | TATAAT at -10 region; DNA unwinds here (A-T rich) |
| -35 region | TTGACA; first contact point of RNA polymerase |
| Prokaryotic termination | Rho-independent (GC hairpin + poly-U) or Rho-dependent (ρ helicase) |
| Eukaryotic RNA Pol I | Nucleolus; makes rRNA (28S, 18S, 5.8S); insensitive to α-amanitin |
| Eukaryotic RNA Pol II | Nucleoplasm; makes mRNA; most sensitive to α-amanitin |
| Eukaryotic RNA Pol III | Nucleoplasm; makes tRNA, 5S rRNA; moderately sensitive |
| α-amanitin | Toxin from Amanita phalloides; inhibits RNA Pol II most strongly |
| TATA box (Hogness box) | TATAAA at -25 to -30; eukaryotic promoter element |
| 5' Capping | 7-methylguanosine (m⁷G) cap; protects mRNA; ribosome recognition |
| 3' Polyadenylation | 100-250 adenines (poly-A tail); signal = AAUAAA |
| RNA Splicing | Removal of introns, joining of exons; by spliceosome (snRNPs) |
| GT-AG rule | Introns begin with GU and end with AG (at RNA level) |
| Split genes discovered by | Richard Roberts & Phillip Sharp (1977); Nobel 1993 |
| Alternative splicing | One gene → multiple mRNAs/proteins; Drosophila Dscam → >38,000 mRNAs |
| Genetic code deciphered by | Nirenberg, Khorana, Holley; Nobel 1968 |
| Total codons | 64 (4³); 61 sense + 3 stop |
| Start codon | AUG (Methionine; fMet in prokaryotes) |
| Stop codons | UAA (Ochre), UAG (Amber), UGA (Opal) |
| Single-codon amino acids | Met (AUG) and Trp (UGG) only |
| Genetic code properties | Triplet, non-overlapping, commaless, non-ambiguous, degenerate, universal, unidirectional (5'→3') |
| Wobble hypothesis | Crick (1966); 3rd codon position allows non-standard pairing; fewer tRNAs needed |
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