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		Quiz Me!	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

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Protein Synthesis, Genetic Code, and Regulation of gene expression

A. Protein synthesis (in prokaryotes)

role of mRNA

• 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.

role of ribosome

• 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

role of tRNA

• 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

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Stages of Translation

• View animation of translation
  1. Initiation
     • 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. Elongation
     • 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)
  3. Termination
     • 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!

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B. Genetic Code

• 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)
  

  GCA GCC GCG GCU Ala	AGA AGG CGA CGC CGG CGU Arg	GAC GAU Asp	AAC AAU Asn	UGC UGU Cys	GAA GAG Glu	CAA CAG Gln	GGA GGC GGG GGU Gly	CAC CAU His	AUA AUC AUU Ile
  UUA UUG CUA CUC CUG CUU Leu	AAA AAG Lys	AUG Met	UUC UUU Phe	CCA CCC CCG CCU Pro	AGC AGU UCA UCC UCG UCU Ser	ACA ACC ACG ACU Thr	UGG Trp	UAC UAU Tyr	GUA GUC GUG GUU Val

  
  

Open Reading Frames (ORFs)

• 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

Universality

• 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.
  

  Codon	"Universal" Code	Mammalian Mitochondrial Code	Yeast Mitochondrial Code
  UGA	Stop	Trp	Trp
  AUA	Ile	Met	Met
  CUA	Leu	Leu	Thr
  AGA AGG	Arg	Stop	Arg

  
  

Codon bias

• 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.

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