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Tamarin: Principles of Genetics, Seventh Edition
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III. Molecular Genetics
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11. Gene Expression: Translation
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The McGraw Hill Companies, 2001
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Pept idyl transferase H O OH H N H2C C H C Puromycin N NH OH N NH2 CH2 OH N N CH3 CH3 O N N N A site O O CH3
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Peptidyl tRNA O
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P site
H R O Amino Amino Amino acid acid acid N C C H
H2C C H C
Peptidyl puromycin NH OH
CH2 OH P site N
N CH3 CH3
A site
Puromycin is bound to the A site of the ribosome. A peptide bond then forms. Further elongation is prevented, and the chain is terminated.
Tamarin: Principles of Genetics, Seventh Edition
III. Molecular Genetics
11. Gene Expression: Translation
The McGraw Hill Companies, 2001
Eleven
Gene Expression: Translation
Figure 11.15 Space- lling model of EF-Tu bound with (a) GDP and (b) GTP, showing the change in the protein s structure. Yellow, blue, and red are domains of the protein. The GTP and GDP are in white, with a magnesium ion, Mg2+, in green. When EF-Tu is bound with GDP, there is a visible hole in the molecule. The hole disappears when GTP is bound. The aminoacyl-transfer RNA is believed to bind between the red and yellow domains. (Courtesy of Rolf Hilgenfeld.)
charged transfer RNA has had an amino acid attached at the expense of the hydrolysis of an ATP to AMP PP. There is some evidence that the action of EF-Tu hydrolyzes two GTPs.
fMet
Termination
5 5 tRNA UA C AAA AUG UUU 5 30S E site Figure 11.16 P site A site mRNA 3
Nonsense Codons
Termination of protein synthesis in both prokaryotes and eukaryotes occurs when one of three nonsense codons appears in the A site of the ribosome. These codons are UAG (sometimes referred to as amber), UAA (ochre), and UGA (opal). ( Amber, or brown stone, is the English translation of the name Bernstein, a graduate student who took part in the discovery of UAG in R. H. Epstein s lab at the California Institute of Technology. Ochre and opal are tongue-in-cheek extensions of the rst label.) In prokaryotes, three proteins called release factors (RF) are involved in termination,and a GTP is hydrolyzed to GDP Pi. When a nonsense codon enters the A site on the ribosome, a release factor recognizes it. RF1 and RF2 are class 1 release factors: They recognize stop codons and then promote hydrolysis of the bond between the terminal amino acid and its tRNA in the P site. Class 2 release factors (RF3) do not recognize stop codons, but they stimulate class 1 release factors to act. RF1 recognizes the stop codons UAA and UAG, and RF2 recognizes UAA and UGA ( g. 11.20). Both do so because they have tripep-
A ribosome with two transfer RNAs attached. In this case, the second codon (UUU) is for the amino acid phenylalanine. The two amino acids are next to each other.
protein synthesis, two GTPs are hydrolyzed per peptide bond: one GTP in the release of EF-Tu from the A site, and one GTP in the translocational process of the ribosome after the peptide bond has formed. In addition, every
Tamarin: Principles of Genetics, Seventh Edition
III. Molecular Genetics
11. Gene Expression: Translation
The McGraw Hill Companies, 2001
Information Transfer
fMet
H H C H S H C O H C H N H C C H H H O C H :N H H H C C H H H O C H H
place with the help of IF3, which rebinds to the 30S subunit, and a ribosome recycling factor (RRF). Table 11.1 compares prokaryotic and eukaryotic translation.
Rate and Cost of Translation
As mentioned, the average speed of protein synthesis is about fteen peptide bonds per second in prokaryotes. Discounting the time for initiation and termination, an average protein of three hundred amino acids is synthesized in about twenty seconds (the released protein forms its nal structure spontaneously or is modi ed with the aid of other proteins, as we shall see).An equivalent eukaryotic protein takes about 2.5 minutes to be synthesized.The energy cost is at least four high-energy phosphate bonds per peptide bond (two from an ATP during transfer RNA charging, and two from GTP hydrolysis during transfer RNA binding at the A site and translocation), or about twelve hundred high-energy bonds per protein.This cost is very high about 90% of the energy production of an E. coli cell goes into protein synthesis. A high energy cost is presumably the price a living system has to pay for the speed and accuracy of its protein synthesis.
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