Chapter 25 Using the Genetic Code

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Chapter 25Using the Genetic Code
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25.2 Related Codons Represent Chemically Similar
Amino Acids

• Sixty-one of the sixty-four possible triplets
  code for twenty amino acids.
• Three codons (stop codons) do not represent amino
  acids and cause termination.

FIGURE 01 The genetic code is triplet
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25.2 Related Codons Represent Chemically Similar
Amino Acids

• The genetic code was frozen at an early stage of
  evolution and is universal.
• Most amino acids are represented by more than one
  codon.

FIGURE 02 Amino acids have 1-6 codons each
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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.

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25.3 CodonAnticodon Recognition Involves
Wobbling

• Multiple codons that represent the same amino
  acid most often differ at the third base position
  (the wobble hypothesis).

FIGURE 03 Third bases have the least influence
on codon meanings
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25.3 CodonAnticodon Recognition Involves
Wobbling

• The wobble in pairing between the first base of
  the anticodon and the third base of the codon
  results from looser monitoring of the pairing by
  rRNA nucleotides in the ribosomal A site.

FIGURE 04 Wobble in base pairing allows G-U
pairs to form
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FIGURE 05 Codonanticodon pairing involves
wobbling at the third position
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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 06 Both ends of tRNA are generated by
processing
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25.5 tRNA Contains Modified Bases

• tRNAs contain over 90 modified bases.
• 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 07 Base modifications in tRNA vary in
complexity.
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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.

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25.6 Modified Bases Affect AnticodonCodon
Pairing

• Modifications in the anticodon affect the pattern
  of wobble pairing and therefore are important in
  determining tRNA specificity.

FIGURE 09 Modification to 2-thiouridine
restricts pairing to A
FIGURE 08 Inosine pairs with three bases
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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 11 Changes in the genetic code in
mitochondria can be traced in phylogeny
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25.7 There Are Sporadic Alterations of the
Universal Code

• In nuclear genomes, the changes usually affect
  only termination codons.

FIGURE 10 Changes in the genetic code usually
involve Stop/None signals
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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 12 SelB is specific for Seleno-Cys-tRNA
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25.9 tRNAs Are Selectively Paired with Amino
Acids by Aminoacyl-tRNA Synthetases

• Aminoacyl-tRNA synthetases are a family of
  enzymes that attach amino acid to tRNA,
  generating aminoacyl-tRNA 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.

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25.9 tRNAs Are Selectively Paired 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 13 An aminoacyl-tRNA synthetase charges
tRNA with an amino acid
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25.10 Aminoacyl-tRNA Synthetases Fall into Two
Families

• Aminoacyl-tRNA synthetases are divided into class
  I and class II families based on mutually
  exclusive sets of sequence motifs and structural
  domains.

FIGURE 16 Class I (Glu-tRNA synthetase) Class
II (Asp-tRNA synthetase)
FIGURE 14 Separation of tRNA synthetases into
two classes
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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.

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FIGURE 17 Kinetic proofreading reduces errors
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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 18 Synthetases use chemical proofreading
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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 to which it
  responds.

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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.

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FIGURE 21 Nonsense mutations can be suppressed
by a tRNA with a mutant anticodon
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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 22 Missense suppressors compete with
wild type
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25.13 There Are Nonsense Suppressors for Each
Termination Codon

• Each type of nonsense codon is suppressed by a
  tRNA with a mutated anticodon.
• Some rare suppressor tRNAs have mutations in
  other parts of the molecule.

FIGURE 23 Suppressors have anticodon mutations
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25.14 Suppressors May Compete with Wild-Type
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.

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FIGURE 24 Nonsense suppressors read through
natural termination codons
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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 The ribosome selects aminoacyl-tRNAs
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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.

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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 26 A tRNA that slips one base in pairing
with a codon causes a frameshift that
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25.16 Frameshifting Occurs at Slippery Sequences
FIGURE 27 Bypassing skips between identical
codons
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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 29 In bypass mode, a ribosome with its P
site occupied can stop translation
FIGURE 28 Frameshifting controls translation
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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.