Using the Genetic Code

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Chapter 9

• Using the Genetic Code

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9.1 Introduction

• The sequence of a coding strand of DNA is read in
  the direction from 5' to 3'.
• This corresponds to the amino acid sequence of a
  polypeptide read from N-terminus to C-terminus.

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9.2 Related Codons Represent Related Amino Acids

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

Figure 9.01 The genetic code is triplet.
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9.2 Related Codons Represent Related 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.
• The multiple codons for an amino acid are usually
  related.
• Related amino acids often have related codons,
  minimizing the effects of mutation.

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Figure 9.02 The number of codons for each amino
acid does not correlate closely with its
frequency of use in proteins.
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9.3 CodonAnticodon Recognition Involves Wobbling

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

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9.3 CodonAnticodon Recognition Involves Wobbling

• The wobble in pairing between the first base of
  the anticodon and the third base of the codon
  results from the structure of the anticodon loop.

Figure 9.04 G-U pairs form at the third codon
base.
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9.3 CodonAnticodon Recognition Involves Wobbling
Figure 9.5 Codon-anticodon pairing involves
wobbling at third position.
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9.4 tRNA Contains Modified Bases

• tRNAs contain gt50 modified bases.
• Modification usually involves direct alteration
  of the primary bases in tRNA.
• There are some exceptions in which a base is
  removed and replaced by another base.

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9.4 tRNA Contains Modified Bases
Figure 9.06 Base modifications in tRNA vary in
complexity.
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9.5 Modified Bases Affect AnticodonCodon Pairing

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

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9.5 Modified Bases Affect AnticodonCodon Pairing
Figure 9.07 Inosine pairs with three bases.
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9.5 Modified Bases Affect AnticodonCodon Pairing
Figure 9.8 Modification to 2-thiouracil
restricts paring to A alone because only one
H-bond can form with G.
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9.6 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.
• In nuclear genomes, the changes are sporadic and
  usually affect only termination codons.

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9.6 There Are Sporadic Alterations of the
Universal Code
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9.6 There Are Sporadic Alterations of the
Universal Code
Figure 9.10 Mitochondria have changes in the
genetic code.
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9.7 Novel Amino Acids Can Be Inserted at Certain
Stop Codons

• Changes in the reading of specific codons can
  occur in individual genes.
• The insertion of seleno-Cys-tRNA at certain UGA
  codons requires several proteins to modify the
  Cys-tRNA and insert it into the ribosome.
• Pyrrolysine can be inserted at certain UAG codons.

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9.7 Novel Amino Acids Can Be Inserted at Certain
Stop Codons
SelB is an elongation factor specific for
Seleno-Cys-tRNA.
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9.8 tRNAs Are Charged with Amino Acids by
Synthetases

• Aminoacyl-tRNA synthetases are enzymes that
  charge tRNA with an amino acid to generate
  aminoacyl-tRNA in a two-stage reaction that uses
  energy from ATP.
• There are twenty aminoacyl-tRNA synthetases in
  each cell. Each charges all the tRNAs that
  represent a particular amino acid.
• Recognition of a tRNA is based on a small number
  of points of contact in the tRNA sequence.

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9.8 tRNAs Are Charged with Amino Acids by
Synthetases
Figure 9.12 The charging reaction uses ATP.
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9.9 Aminoacyl-tRNA Synthetases Fall into Two
Groups

• Aminoacyl-tRNA synthetases are divided into the
  class I and class II groups by sequence and
  structural similarities.

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9.9 Aminoacyl-tRNA Synthetases Fall into Two
Groups
Figure 9.13 Class I (Glu-tRNA synthetase) and
Class II (Asp-tRNA synthetase).
Photo courtesy of Dino Moras, Institute of
Genetics and Molecular and Cellular Biology
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9.10 Synthetases Use Proofreading to Improve
Accuracy

• Specificity of recognition of both amino acid and
  tRNA is controlled by aminoacyl-tRNA synthetases.
• They function through proofreading reactions that
  reverse the catalytic reaction if the wrong
  component has been incorporated.

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9.10 Synthetases Use Proofreading to Improve
Figure 9.16 Synthetases use chemical
proofreading.
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9.11 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.
• Each type of nonsense codon is suppressed by
  tRNAs with mutant anticodons.

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9.11 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
• readthrough at a natural termination codon

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9.11 Suppressor tRNAs Have Mutated Anticodons
That Read New Codons
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9.11 Suppressor tRNAs Have Mutated Anticodons
That Read New Codons
Figure 9.20 Nonsense suppression causes
readthrough.
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9.11 Suppressor tRNAs Have Mutated Anticodons
That Read New Codons

• 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.

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9.11 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.

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9.11 Suppressor tRNAs Have Mutated Anticodons
That Read New Codons
Figure 9.21 Missense suppressors compete with
wild type.
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9.12 Recoding Changes Codon Meanings

• Changes in codon meaning can be caused by mutant
  tRNAs or by tRNAs with special properties.

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9.12 Recoding Changes Codon Meanings
Figure 9.22 Special or mutant tRNAs change
meaning.
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9.12 Recoding Changes Codon Meanings

• The reading frame can be changed by frameshifting
  or bypassing, both of which depend on properties
  of the mRNA.

Figure 9.23 Frameshifts can suppress termination.
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9.12 Recoding Changes Codon Meanings
Figure 9.24 Bypassing skips between identical
codons.
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9.13 Frameshifting Occurs at Slippery Sequences

• The reading frame may be influenced by the
  sequence of mRNA and the ribosomal environment.
• 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.
• Some mutant tRNA suppressors recognize a four
  base codon instead of normal three bases.

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9.13 Frameshifting Occurs at Slippery Sequences
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9.14 Bypassing Involves Ribosome Movement

• A ribosome encounters a GGA codon adjacent to a
  stop codon in a specific stem-loop structure.
• It moves directly to a specific GGA downstream
  without adding amino acids to the polypeptide.

Figure 9.26 A ribosome can bypass a sequence of
mRNA.