Chapter 12
Protein Synthesis: Translation of the Genetic Message
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SUMMARY
Section 12.1
Protein translation involves 3 types of RNA and many protein factors.
Section 12.2
The genetic code is based on a series of three bases coding for an amino acid.
The code is nearly universal in all organisms from viruses through humans. The
code has no punctuation, meaning the mRNA is read three bases at a time with
no spaces in between. The code is non-overlapping as well, meaning that each
base is part of only one codon.
Section 12.3
Before amino acids can be incorporated into a peptide, they must be activated.
Section 12.4
The unique and elegant structure of the ribosome allows the binding of
aminoacyl-tRNA molecules and mRNA. The ribosome catalyzes the nucleophilic
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In chain elongation, the second amino acyl-tRNA binds to the A-site. This amino
acid’s -amino group performs a nucleophilic attack on the carbonyl group of the
N-formyl-methionine in the peptidyl transfer reaction. In a translocation step, the
Section 12.5
Eukaryotic translation involves many more protein factors than the corresponding
translation in prokaryotes
Both the 5’–Cap and the 3’ poly-A tail are involved in orienting the ribosome close
to the correct AUG used as the start codon. There is no Shine-Dalgarno
Section 12.6
Proteins are usually modified after their initial translation.
Section 12.7
Proteins are degraded in subcellular organelles, such as lysosomes, or in
macromolecular structures called proteasomes.
Protein Synthesis: Translation of the Genetic Message 3
Many proteins are targeted for destruction by being bound to a protein called
LECTURE NOTES
As with the material of the previous two chapters, most students will have been
introduced to translation in earlier courses, particularly in beginning biology courses, but
they are unlikely to have gone into any of the molecular details. since all three
LECTURE OUTLINE
I. Overview of translation
A. Amino acid activation
B. Chain initiation, elongation, and termination
II. The genetic code
A. Triplet codons
1. Nonoverlapping
B. Codon-anticodon pairing and wobble
III. Amino acid activation
IV. Translation in prokaryotes
A. Ribosomal architecture
1. Two subunits
C. Chain elongation
1. P, A, and E sites
2. Function of elongation factors
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3. Disassembly of ribosomal complex
E. Ribosome as a ribozyme
F. Polysomes – coupling of transcription & translation
V. Translation in eukaryotes
A. Chain initiation
1. Eukaryotic initiation factors
4. Assembly of initiation complex
B. Chain elongation
1. Eukaryotic elongation factors
D. Selenocysteine
E. Coupled transcription & translation in eukaryotes?
VI. Posttranslational modification of proteins
A. Removal of N-formylmethionine
B. Leader sequences
ANSWERS TO PROBLEMS
12.1 Translating the Genetic Message
1. See Figure 12.1.
12.2 The Genetic Code
2. A code in which two bases code for a single amino acid allows for only 16 (4 × 4)
possible codons, which is not adequate to code for 20 amino acids.
3. A degenerate code is one in which more than one triplet can specify a given
amino acid.
4. In the binding assay technique, various tRNA molecules, one of which is
Protein Synthesis: Translation of the Genetic Message 5
factors. A release factor not only blocks the binding of a new aminoacyl-tRNA but
also affects the activity of the peptidyl transferase, so that the bond between the
carboxyl end of the peptide and the tRNA is hydrolyzed.
7. Note that the sequence in the codon of mRNA is reversed because mRNA
synthesis is antiparallel.
(a) Position 1 has an intermediate effect. For purine changes, a different amino acid
results in all cases. The changes tend to be conservative, with only four of the 16
8. The concept of wobble specifies that the first two bases of a codon remain the
same, while there is room for variation in the third base. This is precisely what is
observed experimentally.
9. Hypoxanthine is the most versatile of the wobble bases; it can base pair with
adenine, cytosine, or uracil.
10. It is quite reasonable. When codons for a given amino acid have one or two
nucleotides in common, a mutation is less likely to give rise to a nonfunctional
protein. The survival value of such a feature guarantees its selection in evolution.
11. An ambiguous code would allow for variation in the amino acid sequence of
proteins. Consequently, there would be variation in function, including a number
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12.3 Amino Acid Activation
15. The hydrolysis of ATP to AMP and PPi provides the energy to drive the activation
step.
16. Proofreading in amino acid activation takes place in two stages. The first requires
a hydrolytic site on the aminoacyl-tRNA synthetase; incorrect amino acids that
17. The following factors ensure fidelity in protein synthesis. Aminoacyl-tRNA
formation includes a high degree of enzyme specificity to connect the right amino
acid to the right tRNA, proofreading in the formation of some aminoacyl-
18. A separate synthetase exists for each amino acid, and this synthetase functions
for all of the different tRNA molecules for that amino acid.
19. The linkage of amino acids to tRNA is as an aminoacyl ester.
20. Proofreading at the activation step allows for selection of both the amino acid and
12.4 Prokaryotic Translation
22. Peptidyl transferase catalyzes the formation of a new peptide bond in protein
synthesis. The elongation factors, EF-Tu and EF-Ts, are required for binding of
aminoacyl tRNA to the A site. The third elongation factor, EF-G, is needed for the
translocation step in which the mRNA moves with respect to the ribosome,
Protein Synthesis: Translation of the Genetic Message 7
25. The A site and the P site on the ribosome are both binding sites for charged
tRNAs taking part in protein synthesis. The P (peptidyl) site binds a tRNA to
26. Puromycin terminates the growing polypeptide chain by forming a peptide bond
with its C-terminus, which prevents the formation of new peptide bonds (see
Figure 12.14).
27. The stop codons bind to release factors, proteins that block binding of aminoacyl
tRNAs to the ribosome, and to release the newly formed protein.
31. Methionine bound to tRNAfmet can be formylated, but methionine bonded to
tRNAmet cannot be.
32. Different tRNAs and different factors are involved. Initiation requires IF-2, which
recognizes fmet-tRNAfmet but not met-tRNAfmet. Conversely, in elongation, EF-Tu
recognizes metRNAmet but not fmet-tRNAfmet.
35.
(a) Activation cycles needed for a protein with 150 AA: 150.
36. Four high-energy phosphate bonds per amino acid: two in aminoacyl-tRNA
formation, one in elongation with EF-Tu, and one in translocation from the A to
the P site, involving EF-G. Forming a peptide bond requires about 5 kcal/mol.
This is an expenditure of about 30 kcal/mol peptide bonds. This is the price of
low entropy and high fidelity.
37. Not very precisely. Ignoring any editing or proofreading costs, a maximum value
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tRNA are relatively long-lived and available for repeated protein syntheses.
38. The fact that peptidyl transferase is one of the most conserved sequences in all
of biology may indicate that it evolved very early in evolution and that it is so
critical for all living organisms that it cannot be modified.
39. The less highly purified ribosome preparations contained polysomes, which are
more active in protein synthesis than single ribosomes.
other. This facilitates formation of the next peptide bond.
43. A virus takes over the protein-synthesizing machinery of the cell. It uses its own
nucleic acids and the cell’s ribosomes.
44. The other amino acids found in proteins are created by modifying one of the
twenty standard amino acids after the protein is made. Selenocysteine is formed
while the amino acid is bound to tRNA. Thus, this amino acid is inserted into the
12.5 Eukaryotic Translation
46. Pro-X-Thr is conserved in RF-1 and Ser-Pro-Phe is conserved in RF-2.
47. The sequence Gly-Gly-Gln.
48. Similarities between protein synthesis in bacteria and protein synthesis in
eukaryotes: same start and stop codons; same genetic code; same chemical
49. The original N-terminal methionine can be removed by posttranslational
modification.
50. Puromycin would be useful for treatment of a viral infection, but chloramphenicol
would not. Viral mRNAs are translated by eukaryotic translation systems, so one
Protein Synthesis: Translation of the Genetic Message 9
52. Some mutations can introduce stop codons. It is useful to a cell to have some
mechanism to suppress the formation of incomplete proteins.
53. New protein synthesis is involved in long-term memories.
54. A critical role is played by the transcription factor CREB (chapter 11) in turning
12.6 Posttranslational Modification of Proteins
57. Hydroxyproline is formed from proline, an amino acid for which there are four
codons, by posttranslational modification of the collagen precursor.
N-terminal amino acid.
59. Peptides of the immune system that are displayed on the surface of the major
histsocompatibility complexes
60. Proteins that bind to proteins while they are being synthesized and aid in their
12.7 Protein Degradation
64. Ubiquitin is a small polypeptide (76 amino acids) that is highly conserved in
eukaryotes. When ubiquitin is linked to a protein, it marks that protein for
degradation in a proteasome.
65. If proteins to be degraded did not have some signal marking them, the process
would take place more randomly and thus be less efficient.
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sometimes differences in codons for the same amino acid do affect the overall
protein product.
69. If the silent mutation is in an exonic splicing enhancer, then the splicing out of
introns could be incorrect and the correct exon could be skipped.
70. Silent mutations in the mRNA for the enzyme control secondary structures of the
mRNA, which controls fast and how often the mRNA is translated, leading to