Translation & the Genetic Code
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Last revised: Monday, March 13, 2000
Ch. 11 (p. 226-233) in Prescott et al, Microbiology, 4th Ed.Note: These notes are provided as a guide to topics the instructor hopes to cover during lecture. Actual coverage will always differ somewhat from what is printed here. These notes are not a substitute for the actual lecture!Copyright 2000. Thomas M. Terry
Protein Synthesis, Genetic Code, and Regulation of gene expression
A. Protein synthesis (in prokaryotes)
- carries coding information for amino acids = codons, 3 adajacent nucleotide bases
- Example: AAA, AGU, etc.
- leader sequence on mRNA (called Shine-Dalgarno sequence) binds to complementary sequence on small ribosome subunit.
- acts as a "decoding box" or "tape player" for the information in mRNA
- 30S & 50S subunits (= 70S)
- 30S has 16S RNA + 21 proteins
- 50S has 23S & 5S RNA + 34 proteins
- View model of ribosome 1
- View model of ribosome 2
- structure: 4 loops, anticodon, AA binding site
- ~ 60 types in bacteria (>100 in mammals)
- only 73-93 nucleotides long
- some modified bases: pseudouridine, inosine, others
- modified after transcription
- extensive hairpin loops
- View model of tRNA
- anticodon site: recognizes codon on mRNA
- AA added by enzyme: AA-tRNA activating enzymes
- ATP required, forms AA-AMP + PP, then AA-tRNA + AMP
Stages of Translation
- View animation of translation
- 30S initiates binding to mRNA
- locates Shine-Dalgarno sequence (3-9 bases near 5' end of mRNA)
- ribosome finds first AUG codon
- 50S ribosome binds
- tRNA carries N-formylmethione to first position
- View animation of initiation (requires access to The Biology Place)
- 2 adjacent sites on ribosome: P and A site
- A site accepts a new tRNA-AA
- Psite holds existing chain
- peptide transferred from P site tRNA to A-site AA
- enzyme activity is in ribosomal RNA, not protein
- also required: Energy (GTP) and elongation factors
- View animation of elongation (requires access to The Biology Place)
- reach a "stop codon" UAG, UAA, or UGA
- no t-RNAs for release, but release factors required
- View animation of termination (requires access to The Biology Place)
- Net cost: 4 phosphate bonds/amino acid added!
- AUG = universal "start" codon
- UAG, UAA, UGA = "stop" codons
- A few messages in bacteria use GUG as start, but still need Shine-Dalgarno sequence, still code for N-formylmethionine
- Genetic Code table (arranged to view codons for each amino acid)
- when looking at DNA sequences, see many AUG (approx. 1 in every 64). But most of these are not actual "start" codons. Why?
- 3 possible reading frames. Also, AUG serves as ordinary codon for methionine.
- Most proteins are long (100s to thousands of bases). Look for AUG followed by long region without "stop" codon = ORF
- Computer programs used to find ORFs from DNA sequences
- ORF = gene, defined by computer search
- originally thought all organisms use identical codons
- But mitochondria of eukaryotes (except plants) use slightly different assignments for a few codons. Some examples of non-universal codons are shown in the table below.
UGA Stop Trp Trp AUA Ile Met Met CUA Leu Leu Thr AGA
Arg Stop Arg
- original assumption: if multiple codons for an amino acid, expect equal frequency of use
- Surprise! Codon use is often highly biased. Eg. E. coli can use AUA, AUU, or AUC to specify isoleucine; but only 1 in 20 times is an isoleucine coded by AUA; 19/20 times encoded by AUU or AUC. So AUA is only rarely used -- may allow evolution to develop alternate codes.
- Consult the codon usage table to find how frequently each codon is used for any organism in this extensive database.