The genetic code and translation

Central Dogma of Molecular Biology

Replication makes DNA copies; transcription converts DNA to RNA; translation converts mRNA into protein.

Coupling vs Compartmentalization (Prokaryotes vs Eukaryotes)

Prokaryotes couple transcription and translation; eukaryotes separate them (nucleus vs cytoplasm).

Codon Definition

A codon is a sequence of three mRNA nucleotides that specifies one amino acid.

Start Codon

AUG is the start codon and codes for methionine (fMet in bacteria).

Stop Codons

UAA, UAG, and UGA are stop (nonsense) codons that terminate translation.

Reason for 3-Nucleotide Codons

4³ = 64 combinations → enough to encode 20 amino acids + stop codons.

Redundancy (Degeneracy) of Genetic Code

Multiple codons encode the same amino acid; largely due to wobble at the 3rd position.

Wobble Position

The 3rd base of the codon (1st of anticodon) can vary without changing the amino acid.

Amino Acids With Six Codons

Leu, Ser, Arg have six codons due to wobble and multiple tRNAs.

Universality of the Genetic Code

Genetic code is nearly universal; most organisms use same codon assignments.

Mitochondrial Genetic Code Exceptions

AUA = Met; UGA = Trp in mitochondria; evidence for endosymbiotic origin.

tRNA Function

tRNA links mRNA codons to amino acids using anticodons and amino acid attachment at 3' CCA end.

Number of tRNAs

~45 tRNAs recognize 61 codons due to wobble base pairing.

Adaptor Hypothesis

Crick & Hoagland proposed tRNA as the adaptor recognizing codons and carrying amino acids.

Aminoacyl-tRNA Synthetase Function

Enzymes that attach correct amino acid to its tRNA (charging). One per amino acid (~20).

Charging tRNA – Step 1 (Activation)

Amino acid + ATP → aminoacyl-AMP (activation).

Charging tRNA – Step 2 (Transfer)

Amino acid transferred from aminoacyl-AMP to tRNA → charged tRNA + AMP.

Important Features of tRNAs

tRNA has unusual bases, anticodon loop, 3' CCA, carries one specific amino acid.

Ribosome Function

Coordinates pairing of tRNA anticodons to mRNA codons and catalyzes peptide bonds.

Ribosome Subunits

Prokaryotes: 30S + 50S = 70S; Eukaryotes: 40S + 60S = 80S.

Shine-Dalgarno Sequence

Prokaryotic ribosome-binding site on mRNA recognized by 16S rRNA.

Initiator tRNA in Bacteria

tRNA^fMet carries formyl-methionine to start translation.

Initiator tRNA in Eukaryotes

tRNA^Met carries unmodified methionine.

Kozak Sequence

Eukaryotic consensus sequence around AUG that enhances start codon recognition.

5' Cap–Dependent Scanning (Eukaryotes)

Small ribosomal subunit binds 5′ cap then scans to first AUG in Kozak context.

Ribosomal Sites

A site (aminoacyl), P site (peptidyl), E site (exit).

Translation Initiation

Assembly of mRNA + ribosomal subunits + initiator tRNA + initiation factors.

Translation Elongation

tRNA enters A site → peptide bond forms → ribosome translocates → old tRNA exits E site.

Energy for Translation

GTP hydrolysis powers initiation and elongation steps.

Polyribosomes (Polysomes)

Multiple ribosomes simultaneously translating the same mRNA.

Translation Termination

Stop codon enters A site → release factors bind → polypeptide, tRNA, and mRNA released.

Release Factors

Proteins mimicking tRNA shape that recognize stop codons; not tRNAs.

Peptide Directionality

N-terminus → C-terminus corresponds to mRNA 5' → 3'.

Co-linearity

DNA coding strand, mRNA codons, and protein amino acid sequence correspond directly.

Protein Folding

Folding begins during translation; sequence determines final 3D structure.

Tetracycline Mechanism

Antibiotic that binds 30S subunit and blocks aminoacyl-tRNA entry.

Aminoglycosides Mechanism

Bind 30S subunit and interfere with ribosomal assembly.

Erythromycin/Clindamycin Mechanism

Bind 50S subunit and inhibit protein synthesis.

Prokaryotic vs Eukaryotic mRNA Features

Prokaryotes: polycistronic, no 5' cap. Eukaryotes: monocistronic, 5' cap + scanning.

Prokaryotic Initiator Amino Acid

Formyl-methionine (fMet).

Eukaryotic Initiator Amino Acid

Methionine (unmodified).