Central Dogma: Transcription and Translation

Overview

Chapter explains how genetic information flows from DNA to protein (Central Dogma).
Focus on transcription (DNA to RNA) and translation (RNA to protein), genetic code, and differences between prokaryotic and eukaryotic gene expression.
Emphasizes roles of rRNA, tRNA, mRNA, RNA polymerase, ribosomes, and RNA processing (splicing, caps, tails).

DNA → RNA → Protein summarizes gene expression.
Two phases: transcription (RNA polymerase makes mRNA) and translation (ribosome synthesizes polypeptide).
Proteins are the functional tools of heredity, produced according to DNA instructions.

rRNA: structural and catalytic component of ribosomes; site of polypeptide assembly.
tRNA: transports and positions amino acids; anticodon base-pairs with mRNA codons.
mRNA: carries gene-encoded sequence from nucleus (eukaryotes) to ribosomes for translation.

RNA Type	Primary Function
rRNA	Forms ribosome structure and catalytic sites for peptide bond formation
tRNA	Carries amino acids and matches anticodons to mRNA codons
mRNA	Conveys nucleotide sequence of gene to ribosome for translation

RNA polymerase binds promoter, unwinds DNA, synthesizes RNA complementary to template strand.
Only one DNA strand (template/antisense) is transcribed; coding (sense) strand matches RNA (T→U).
Synthesis proceeds 5′→3′ without primer; bacterial RNA polymerase lacks proofreading.
Termination often via GC hairpin followed by U-run causing polymerase pausing and dissociation.

Step	Key Points
Initiation	Polymerase binds promoter (σ factor in bacteria); TATA/TATAAA motifs help position start
Elongation	Transcription bubble (~17 bp) moves at ~50 nt/sec; RNA-DNA hybrid stabilizes synthesis
Termination	GC hairpin + U stretch or protein factors cause release of transcript

5′ cap: 5′–5′ linked GTP protects mRNA and aids ribosome binding.
3′ poly-A tail: ~250 A residues added after cleavage; protects from degradation.
Splicing: introns removed from primary transcript; exons joined to form mature mRNA.

Modification	Function
5′ Cap	Protects transcript and facilitates ribosome recognition
3′ Poly-A Tail	Stabilizes transcript and improves translation efficiency
Splicing	Removes introns; joins exons to create coding mRNA

Codons: triplets of nucleotides specify amino acids; code is read continuously, no punctuation.
64 triplets encode 20 amino acids plus start/stop signals; redundancy exists (synonymous codons).
Start codon: AUG (methionine); stop codons: UAA, UAG, UGA.
Universality: code conserved across organisms, enabling gene transfer and genetic engineering.
Exceptions: mitochondrial, chloroplast, and certain protist codes have slight differences (e.g., UGA = Trp in mitochondria).

Feature	Notes
Codon Size	Triplet (3 nucleotides) — shown by frameshift experiments
Start/Stop	AUG = Start/Methionine; UAA/UAG/UGA = Stop
Redundancy	Most amino acids have multiple codons; third-base wobble allows fewer tRNAs
Universality	Nearly universal; some organelles deviate slightly

Ribosome structure: small and large subunits with three functional sites: A (aminoacyl), P (peptidyl), E (exit).
Initiation:
- Prokaryotes: initiator tRNA carries N-formylmethionine (fMet); leader sequence positions ribosome.
- Eukaryotes: initiator tRNA carries methionine; 5′ cap directs ribosome to first AUG.
Elongation:
- Aminoacyl-tRNA synthetases (activating enzymes) attach correct amino acids to tRNAs.
- tRNA anticodon pairs with mRNA codon at A site; peptidyl transferase forms peptide bond.
- Translocation shifts ribosome three nucleotides; empty tRNA moves to E site and exits.
Termination:
- Release factors recognize stop codons, cleave polypeptide from tRNA, and release complex.
Polysomes: multiple ribosomes translate a single mRNA simultaneously in prokaryotes and eukaryotes.

Stage	Key Components/Events
Initiation	Initiator tRNA (fMet in bacteria, Met in eukaryotes), small subunit, initiation factors
Elongation	Aminoacyl-tRNA synthetases, elongation factors, peptidyl transferase, translocation
Termination	Release factors recognize stop codon, release completed polypeptide

One enzyme type per amino acid (20 total) links amino acid to corresponding tRNA(s).
Enzyme recognizes both the amino acid and tRNA anticodon/structure.
Some synthetases charge multiple tRNA isoacceptors for the same amino acid.

Introns: noncoding sequences within genes removed from primary transcript.
Exons: coding segments joined after splicing to form mature mRNA.
Discovery involved cDNA–genomic DNA hybridization revealing looped-out introns.
Introns can be much larger than exons; splicing is essential before mRNA export and translation.

Term	Definition
Intron	Noncoding sequence removed from primary RNA transcript
Exon	Coding sequence retained and joined in mature mRNA
Splicing	Enzymatic removal of introns and ligation of exons

Introns: common in eukaryotes, rare in bacteria.
mRNA structure: bacterial mRNAs often polycistronic; eukaryotic mRNAs typically monocistronic.
Spatial separation: eukaryotes transcribe in nucleus and export mRNA before translation; bacteria couple transcription and translation.
Initiation signals: bacteria use ribosomal binding site; eukaryotes use 5′ cap and scanning to first AUG.
mRNA processing: eukaryotic mRNAs are capped, polyadenylated, and spliced; bacterial mRNAs generally are not.
Ribosome size: eukaryotic ribosomes slightly larger than bacterial ribosomes.

Aspect	Bacteria	Eukaryotes
Introns	Rare	Common
mRNA Type	Often polycistronic	Usually monocistronic
Transcription/Translation	Coupled (no nucleus)	Separated by nuclear membrane
Initiation	Ribosome binding site	5′ cap scanning to first AUG
mRNA Processing	Minimal	5′ cap, splicing, 3′ poly-A tail

Central Dogma: DNA → RNA → Protein flow of information.
Codon: three-nucleotide mRNA unit specifying an amino acid or stop signal.
Anticodon: three-nucleotide sequence on tRNA complementary to mRNA codon.
RNA polymerase: enzyme synthesizing RNA from DNA template.
Promoter: DNA sequence where RNA polymerase initiates transcription.
Introns/Exons: noncoding/coding segments in eukaryotic genes.
Poly-A tail and 5′ cap: eukaryotic mRNA modifications that stabilize and aid translation.

Memorize the three major RNA types and their functions.
Learn the translation sites (A, P, E) and sequence of events in initiation, elongation, and termination.
Practice reading the codon table; focus on start/stop codons and redundancy patterns.
Understand differences between prokaryotic and eukaryotic gene expression, especially mRNA processing.
Review the roles of aminoacyl-tRNA synthetases and the concept of wobble at the third codon position.