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Chapter 15 The Genetic Code
The code is degenerate (簡併的)
Three rules govern the genetic code
Suppressor mutations can reside in the same or a
different gene
The code is nearly universal
The code is degenerate (簡併的)
Degeneracy (簡併性) : many amino acids are
specified by more than one codon.
Synonyms (同義密碼子): codons specifying
the same amino acid.
Fig 15-1 codon-anticodon pairing of two
tRNA Leu molecules.
Perceiving order in the makeup of the code
The genetic code might have evolved in a way to minimize
deleterious effects of mutations.
1. Codons with pyrimidines in the 2nd position mostly specify
hydrophobic amino acids; while those with purines in the 2nd
position mostly specify hydrophilic amino acids.
2. As the first two positions are both occupied by G or C, any
of the four nucleotides in the 3rd position will specify the
same amino acid.
Wobble in the anticodon
Table 15-2 pairing combinations with the wobble concept
Base in anticodon
Base in codon
G
U or C
C
G
A
U
U
A or G
I
A, U, or C
Does a specific tRNA anticodon would exist for every codon?
1. Highly purified tRNA species of known sequences could
recognize more than one codon.
2. Inosine (I)
Wobble concept (擺動概念)
Francis Crick, 1966
The base at the 5’ end of the anticodon is not as spatially
confined as the other two, allowing it to form hydrogen bonds
with any of the several bases located at the 3’ end of the codon.
Fig. 15-2 wobble base pairing:
ribose-ribose distances for all
the wobble pairs are close to
those of the standard A:U or
G:C pairings.
Fig 15-3 structure of yeast tRNAphe.
The 1st anticodon base is at the end of the stacking interactions
between flat surfaces of the bases, and is perhaps less restricted in
its movement than the other two bases.
How the code was cracked?
Stimulation of amino acid incorporation by synthetic mRNAs
Poly-U
Poly-C
Poly-G
Poly-U codes for polyphenylalanine
A high magnesium concentration circumvents the need for
initiation factors and the special initiator tRNA, allowing chain
elongation to occur without proper signals in the mRNA.
Poly-U was the first synthetic polyribonucleotide discovered to
have mRNA activity.
CCC: proline
AAA: lysine
Poly-G forms strong intra-chain hydrogen bond and does not
interact with ribosome.
Mixed copolymers allowed additional codon assignments
Table 15-3
Such experiments did not reveal the order of nucleotides within
a codon.
Transfer RNA binding to defined trinucleotide codons
Table 15-4
Even in the absence of all the factors required for protein
synthesis, specific aminoacyl-tRNA molecules can bind to
ribosome-mRNA complexes.
Fig 15-5 preparing oligo-ribonucleotides.
Organic synthesis and copying by DNA polymerase I.
Three rules govern the genetic code
1. Codons are read in a 5’ to 3’ direction.
2. Codons are nonoverlapping and the message contains no
gaps.
3. The message is translated in a fixed reading frame, which is
set by the initiation codon.
Three kinds of point mutations alter the
genetic code
Missense mutation (錯義突變): an alteration that
changes a codon specific for one amino acid to a
codon specific for another amino acid.
Nonsense or stop mutation (無義突變): an alteration
causing a chain-termination codon.
Frameshift mutation (移碼突變)
Genetic proof that the code is read in units
of three
Bacteriophage T4
Suppressor mutations can reside in the
same or a different gene
Reverse (back) mutations 回復突變
Suppressor mutations 抑制基因突變
Intragenic suppression
Intergenic suppression
Fig 15-6 (intragenic) suppression of frameshift mutations.
Fig 15-7 nonsense suppression
(intergenic suppression)
The code is nearly universal
With the exception of mitochondral DNA
Table 15-6
Eukaryotic gene regulation at steps after
transcription initiation
The regulation of alternative mRNA splicing can
produce different protein products in different cell
types
Fig 17-27 early transcriptional regulation of Sxl in male and female flies
Pe: promoter for establishment
Pm: promoter for maintenance
Fig 17-28 a cascade of alternative splicing events determines the sex of a fly.
Sxl: splicing repressor
Tra: splicing activator
Expression of the yeast transcriptional factor
Gcn4 is controlled at the level of translation
Fig 17-29 translational control of Gcn4 in
response to amino acid starvation
RNAs in gene regulation
RNA interference (RNAi): short RNAs that can
repress the expression of those genes with sequence
homology to these RNAs.
Translational inhibition of that mRNA
Destruction of that mRNA
Silencing the promoter that directs expression of that
mRNA
Double-stranded RNA (dsRNA) inhibits
expression of genes homologous to that RNA
In C. elegans and in plants
Short interfering RNAs (siRNAs) are produced
from dsRNAs and direct machinery that
switches off genes in various ways.
RISC: RNA-induced silencing complex
Fig 17-30 RNAi silencing
MicroRNAs (miRNAs) control the expression
of some genes during development
miRNAs: 21-22 nts long; arise from large
precursors (about 70-90 nts long) transcribed
from non-protein encoding sequences. These
transcripts contain sequences that form stem
loop structures, which are processed by Dicer
(or DCL1, Dicer-like 1, in plants).
miRNAs lead to the destruction (in plants) or
translational repression (in worms) of target
mRNAs with homology to the miRNAs.