4) the EF-Tu.GTP.aa-tRNA complex binds to the A site, GTP is
hydrolyzed to GDP and Pi and the EF-Tu can then reform
the EF-Tu.EF-Ts complex
Peptidyl transferase transfers the peptide chain from the tRNA at the P
site to the amino group of the amino acid of the tRNA at the A site (figure 15.22).
The next step is translocation of the tRNA with the peptide chain from
the A site to the P site. The process of translocation involves moving
the entire ribosome down 3 nucleotides. In the process, the depleted
tRNA at the P site is moved to the E site before being ejected to the cytoplasm and the tRNA-peptide is moved to the P
site. This leaves the A site open for the next tRNA. This process
requires GTP and an elongation factor (EF-G) sometimes called
translocase. The hydrolysis of the GTP to GDP and Pi allows the release of EF-G.
The process repeats itself until termination occurs (figure 15.22).
The energy cost for protein synthesis is very high. Two GTP are used
in the direct formation of the peptide bonds. One ATP is converted to
AMP and PiPi when the tRNA is charged. This is
equivalent to two more high energy bonds. An average protein of 300 amino acids requires the equivalent of 1200
ATP's for peptide bond formation. In E. coli, 90% of its energy is
spent on protein synthesis. The average speed of production is 20
peptide bonds per second.
Termination occurs when one of three nonsense codons appears in the A
site of the ribosome. They are UAG, UAA, and UGA. When the
termination codon appears in the A site, it is recognized by a
release factor (figure 15.23).
RF-1 - UAA, UAG
RF-2 - UAA, UGA
In prokaryotes, the majority of mRNAs contains the information for
several genes. These RNAs are termed polycistronic. Each gene,
however, is translated independently, each has its own initiation
sequences, etc (figures 15.25 and 15.26).
In eukaryotes, every mRNA contains only one gene, so they are
monocistronic. Because each mRNA needs the 5' cap for recognition by
the ribosome, you can only have one initiation site per RNA in
1) a third release factor RF-3 is required for the breaking of the
linkage of the terminal amino acid to its tRNA to release the
2) GTP is hydrolyzed to GDP + Pi
3) mRNA is released
4) releasing factors disassociate
5) disassociation of the ribosome is aided by one of the original
(IF-3) initiation factors
The genetic code
DNA --------------> RNA -----------> protein
What is the genetic code? How is information that is coded in the DNA
used to direct protein synthesis?
In the experimental procedures used to determine the genetic code, RNA
was used, so the genetic code is given in terms of RNA. As RNA is
exactly complementary to DNA, you can use either DNA codons or RNA
codons. A codon is the coding unit, or the specific base sequence that codes
for an amino acid.
Length of a codon
How many bases are needed to code for an amino acid? If a codon was one
base long, then four amino acids could be coded for. If a codon was 2
bases long = 42 = 16 amino acids could be coded for. If a codon
was 3 bases long = 43 = 64 amino acids could be coded for.
Therefore, at least 3 bases were needed to code for the 20 amino acids
needed for protein synthesis.
To determine the length of a codon, Crick and his coworkers exposed a
T4 phage to a chemical agent that deletes or adds single base pairs.
The complete amino acid sequence of the protein was worked out and in the
pseudowild type, the protein was found to have a group of five amino acid
not found in the wild type.
Results can be interpreted accordingly
C A T C A T C A T C A T C A T
delete one base
C A T A T C A T C A T C A T C (frame is shifted one base)
add new base
C A T A T C A T G C A T C A T (reading frame is restored,
but there are 2 non-normal amino acids)
They found that if 3 nucleotides were added or 3 nucleotides were deleted,
the reading frame was maintained. They then concluded that a codon was a triplet, or consists of
3 bases. These studies also indictaed that there was no internal punctuation or overlap in the genetic code.
In 1961, Nirenberg and Ochoa produced an artificial RNA composed
entirely of uracil, poly(U). Nirenberg and Matthaei took artificail mRNA and were able to synthesize a protein in a cell-free preparation of ribosome. This was found to code for a protein that
was all phenylalanine (figure 15.9).
The other codons were worked out using a statistical analysis of the
predicted ratios of codons from synthesized RNA from specific ratios of
nucleotides. For example, poly(UG), in which U is twice as common as
G, would code for leucine (UUG), valine (GUU), or cysteine (UGU) (figure 15.10).
Even though they could not make precise statements about which codon went
with which amino acid, they could rule out many possibilities.
Eventually, it became possible to make pieces of RNA with the exact
sequence of bases. Nirenberg and Leder used an assay system that consisted of
1) a synthetic trinucleotide
2) ribosomal preparation from E. coli
3) aminoacyl-tRNA in which the amino acid is radioactively labeled
4) high molar Mg
This was called a trinucleotide binding assay (figure 15.11). They performed a series of
experiments that determined absolutely which codon went with each amino
By 1967, all 64 codons had been worked out using these
61 specified amino acids
3 were termination codons
1 was an initiation codon, and also coded for methionine.
There are only 20 amino acids that are coded for by approximately 50
different tRNA and there are 61 codons that specify an amino acid. As
it turns out, some tRNA's can bind at more than one codon. Crick
called this ability "wobble." If inosine is in the first position in the
anticodon of the tRNA, it can bind to uracil, adenosine, or cytosine
in the third position of the codon. Thus this one tRNA recognizes three different codons (figures 15.12 and 15.13). Remember that the codon and anti-codon are anti-parellel. The first position of the codon is at the 5' end of the codon and binds to the third position (3'end) of the anti-codon.
1) the code is a triplet. Each codon consists of a unique
combination of 3 nucleotides.
2) the code has punctuations only at the ends (start and stop).
Start codon is AUG. Stop codons are UAA, UAG, and UGA.
3) most amino acids are specified by more than one codon, so the
code is redundant. For example, UCU, UCC, UCA, UCG, AGU, and
AGC all code for serine. This is true for 18 of the 20 amino
acids. Only methionine and tryptophan are specified by a single
4) the code is consistent. Each one of the codons specifies a
unique amino acid.
5) the code is universal. Viruses, bacteria, plants, and animals
all use the same code. There are some minor variations in
mitochondria and a few fungi.
Last update on 25 November 2004
Provide comments to Dwight Moore at email@example.com
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