Transcript Chapter25_Outline.ppt

Chapter 25
Using the Genetic Code
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
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
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 03: Third bases
have the least influence on
codon meanings
25.3 Codon–Anticodon 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
FIGURE 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 06: Both ends of tRNA are
generated by processing
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.
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 08: Inosine pairs with
three bases
FIGURE 09: Modification to 2-thiouridine
restricts pairing to A
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
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
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
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 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 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
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
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.
FIGURE 17: Kinetic proofreading reduces errors
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
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.
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.
FIGURE 21: 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 22: Missense suppressors
compete with wild type
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
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.
FIGURE 24: Nonsense suppressors read through natural termination
codons
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
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 26: A tRNA that slips
one base in pairing with a
codon causes a frameshift that
25.16 Frameshifting Occurs at Slippery
Sequences
FIGURE 27: Bypassing skips
between identical codons
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 28: Frameshifting
controls translation
FIGURE 29: In bypass mode, a ribosome
with its P site occupied can stop translation
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.