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Chapter 25
Using the Genetic
Code
25.2 Related Codons Represent Chemically
Similar Amino Acids
• 61 of the 64 possible triplets
encode 20 amino acids.
• Three codons (stop
codons) do not represent
amino acids and cause
termination of translation.
Figure 25.01: All the triplet codons have
meaning: 61 represent amino acids and 3
cause termination (stop codons).
25.2 Related Codons Represent Chemically
Similar Amino Acids
• The genetic code was
frozen at an early stage of
evolution and is nearly
universal.
• Most amino acids are
represented by more than
one codon.
Figure 25.02: Some correlation of the
frequency of amino acid use in proteins
with the number of codons specifying the
amino acid is observed.
25.2 Related Codons Represent Chemically
Similar Amino Acids
• The multiple codons for an amino acid are synonymous
and usually related.
• third-base degeneracy – The lesser effect on codon
meaning of the nucleotide present in the third (3′) codon
position.
• Chemically similar amino acids often have related
codons, minimizing the effects of mutation.
25.3 Codon–Anticodon Recognition
Involves Wobbling
• Multiple codons that
represent the same
amino acid most often
differ at the third base
position (the wobble
hypothesis).
Figure 25.03: Third bases have the least
influence on codon meanings.
25.3 Codon–Anticodon Recognition
Involves Wobbling
• The pairing between the
first base of the anticodon
and the third base of the
codon can vary from
standard Watson-Crick
base pairing according to
specific wobble rules.
Figure 25.04: Wobble in base pairing allows G-U
pairs to form between the third base of the
codon and the first base of the anticodon.
25.3 Codon–Anticodon Recognition
Involves Wobbling
Figure 25.05: Codon–anticodon pairing involves wobbling at the third position.
25.4 tRNAs are Processed from Longer
Precursors
• A mature tRNA is
generated by processing a
precursor.
• The 5′ end is generated by
cleavage by the
endonuclease RNAase P.
• The 3′ end is generated by
multiple endonucleolytic
and exonucleolytic
cleavages, followed by
addition of the common
terminal trinucleotide CCA.
Figure 25.06: The tRNA 3 end is
generated by cutting and trimming
reactions, followed by addition of CCA
when this sequence is not coded.
25.5 tRNA Contains Modified Bases
• 81 examples of modified
bases in tRNAs have been
reported.
• Modification usually
involves direct alteration of
the primary bases in tRNA,
but there are some
exceptions in which a base
is removed and replaced
by another base.
Figure 25.07: Each of the four bases in tRNA
can be modified.
25.5 tRNA Contains Modified Bases
• Known functions of modified bases are to confer
increased stability to tRNAs and to modulate their
recognition by proteins and other RNAs in the
translational apparatus.
25.6 Modified Bases Affect Anticodon–
Codon Pairing
• Modifications in the anticodon affect the pattern of wobble
pairing and therefore are important in determining tRNA
specificity.
Figure 25.08: Inosine can
pair with U, C, or A.
Figure 25.09: Modification to 2thiouridine restricts pairing to A
alone because only one H-bond
can form with G.
25.7 There Are Sporadic Alterations of the
Universal Code
• Changes in the universal genetic code have occurred in
some species.
• These changes are more common in mitochondrial
genomes, where a phylogenetic tree can be constructed
for the changes.
Figure 25.11: Changes in the genetic
code in mitochondria can be traced in
phylogeny.
25.7 There Are Sporadic Alterations of the
Universal Code
• In nuclear genomes, the changes usually affect only
termination codons.
Figure 25.10: Changes in the genetic code in bacterial or eukaryotic nuclear genomes
usually assign amino acids to stop codons or change a codon.
25.8 Novel Amino Acids Can Be Inserted at
Certain Stop Codons
• The insertion of selenocysteine at some UGA codons
requires the action of an unusual tRNA in combination
with several proteins.
• The unusual amino acid pyrrolysine can be inserted at
certain UAG codons.
• The UGA codon specifies both selenocysteine and
cysteine in the ciliate Euplotes crassus.
Figure 25.12: SelB is an elongation factor
that specifically binds tRNASec to a UGA
codon that is followed by a stem-loop
structure in mRNA.
25.9 tRNAs Are Charged with Amino Acids
by Aminoacyl-tRNA Synthetases
• Aminoacyl-tRNA synthetases are a family of enzymes
that attach amino acid to tRNA, generating aminoacyltRNA in a two-step reaction that uses energy from ATP.
• Each tRNA synthetase aminoacylates all the tRNAs in an
isoaccepting (or cognate) group, representing a
particular amino acid.
25.9 tRNAs Are Charged with Amino Acids
by Aminoacyl-tRNA Synthetases
• Recognition of tRNA by
tRNA synthetases is based
on a particular set of
nucleotides, the tRNA
“identity set,” that often
are concentrated in the
acceptor stem and
anticodon loop regions of
the molecule.
Figure 25.13: An aminoacyl-tRNA synthetase charges
tRNA with an amino acid.
25.10 Aminoacyl-tRNA Synthetases Fall
into Two Classes
Photo courtesy of Dino Moras,
Institute of Genetics and Molecular
and Cellular Biology (IGBMC).
• Aminoacyl-tRNA synthetases are divided into class I and
class II families based on mutually exclusive sets of
sequence motifs and structural domains.
Figure 25.14: Separation of tRNA
synthetases into two classes possessing
mutually exclusive sets of sequence
motifs and active-site structural domains.
Figure 25.16: Crystal structures show that
class I and class II aminoacyl-tRNA synthetases
bind the opposite faces of their tRNA
substrates.
25.11 Synthetases Use Proofreading to
Improve Accuracy
• Specificity of amino acid-tRNA pairing is controlled by
proofreading reactions that hydrolyze incorrectly formed
aminoacyl adenylates and aminoacyl-tRNAs.
• kinetic proofreading – A proofreading mechanism that
depends on incorrect events proceeding more slowly
than correct events, so that incorrect events are
reversed before a subunit is added to a polymeric chain.
25.11 Synthetases Use Proofreading to
Improve Accuracy
Figure 25.17: Aminoacylation of cognate
tRNAs by synthetase.
25.11 Synthetases Use Proofreading to
Improve Accuracy
• chemical proofreading –
A proofreading mechanism
in which the correction
event occurs after the
addition of an incorrect
subunit to a polymeric
chain, by means of
reversing the addition
reaction.
Figure 25.18: Proofreading by
aminoacyl-tRNA synthetases.
25.12 Suppressor tRNAs Have Mutated
Anticodons That Read New Codons
• A suppressor tRNA typically has a mutation in
the anticodon that changes the codons which it
recognizes.
25.12 Suppressor tRNAs Have Mutated
Anticodons That Read New Codons
• When the new anticodon corresponds to a
termination codon, an amino acid is inserted and
the polypeptide chain is extended beyond the
termination codon.
– This results in nonsense suppression at a site of
nonsense mutation, or in readthrough at a natural
termination codon.
25.12 Suppressor tRNAs Have Mutated
Anticodons That Read New Codons
Figure 25.20: Nonsense mutations can be
suppressed by a tRNA with a mutant anticodon.
25.12 Suppressor tRNAs Have Mutated
Anticodons That Read New Codons
• Missense suppression
occurs when the tRNA
recognizes a different
codon from usual, so that
one amino acid is
substituted for another.
Figure 25.21: Missense suppression occurs when
the anticodon of tRNA is mutated so that it
responds to the wrong codon.
25.13 There Are Nonsense Suppressors for
Each Termination Codon
• Each type of nonsense codon is suppressed by tRNAs
with mutated anticodons.
• Some rare suppressor tRNAs have mutations in other
parts of the molecule.
Figure 25.22: Nonsense suppressor tRNAs
are generated by mutations in the
anticodon.
25.14 Suppressors May Compete with WildType Reading of the Code
• Suppressor tRNAs compete with wild-type tRNAs that
have the same anticodon to read the corresponding
codon(s).
• Efficient suppression is deleterious because it results in
readthrough past normal termination codons.
• The UGA codon is leaky and is misread by Trp-tRNA at
1% to 3% frequency.
25.14 Suppressors May Compete with WildType Reading of the Code
Figure 25.23: Nonsense suppressors
also read through natural
termination codons, synthesizing
polypeptides that are longer than the
wild type.
25.15 The Ribosome Influences the
Accuracy of Translation
• The structure of the 16S
rRNA at the P and A sites
of the ribosome influences
the accuracy of translation.
Figure 25.24: Any aminoacyl-tRNA can be placed in the A
site, but only one that pairs with the anticodon can make
stabilizing contacts with rRNA.
25.16 Frameshifting Occurs at Slippery
Sequences
• The reading frame may be influenced by the
sequence of mRNA and the ribosomal
environment.
• recoding – Events that occur when the meaning
of a codon or series of codons is changed from
that predicted by the genetic code.
– It may involve altered interactions between
aminoacyl-tRNA and mRNA that are influenced by the
ribosome.
25.16 Frameshifting Occurs at Slippery
Sequences
• Slippery sequences allow a
tRNA to shift by one base
after it has paired with its
anticodon, thereby
changing the reading
frame.
• Translation of some genes
depends upon the regular
occurrence of
programmed
frameshifting.
Figure 25.26: A 11 frameshift is
required for expression of the tyb
gene of the yeast Ty element.
25.16 Frameshifting Occurs at Slippery
Sequences
Figure 25.25: A tRNA that slips one base in
pairing with a codon causes a frameshift
that can suppress termination. The
efficiency is usually ~5%.
25.17 Other Recoding Events: Translational
Bypassing and the tmRNA Mechanism to
Free Stalled Ribosomes
• Bypassing involves the capacity of the ribosome to stop
translation, release from mRNA, and resume translation
some 50 nucleotides downstream.
Figure 25.28: In bypass
mode, a ribosome with
its P site occupied can
stop translation.
Figure 25.27: Bypassing
25.17 Other Recoding Events: Translational
Bypassing and the tmRNA Mechanism to
Free Stalled Ribosomes
• Ribosomes that are stalled on mRNA after partial
synthesis of a protein may be freed by the action of
tmRNA, a unique RNA that incorporates features of both
tRNA and mRNA.