Chapter 5
Messenger
RNA
? 5.1 Introduction
? 5.2 Transfer RNA is the adapter
? 5.3 Messenger RNA is translated by ribosomes
? 5.4 The life cycle of bacterial messenger RNA
? 5.5 Translation of eukaryotic mRNA
? 5.6 The 5? end of eukaryotic mRNA is capped
? 5.7 The 3? terminus is polyadenylated
? 5.8 Bacterial mRNA degradation involves multiple enzymes
? 5.9 mRNA degradation involves multiple activities
? 5.10 Sequence elements may destabilize mRNA
? 5.11 Nonsense mutations trigger a surveillance system
Coding region is a part of the gene that represents a
protein sequence.
Coding strand of DNA has the same sequence as
mRNA.
template strand of double-stranded DNA is the one that
is used to specify the sequence of a complementary
single strand of RNA,(The non-template strand is
identical in sequence to the RNA product.)
Transcription is synthesis of RNA on a DNA template.
Translation is synthesis of protein on the mRNA
template.
5.1 Introduction
Figure 5.1 Transcription
generates an RNA which is
complementary to the DNA
template strand and has the
same sequence as the DNA
coding strand,Translation
reads each triplet of bases
into one amino acid,Three
turns of the DNA double
helix contain 30 bp,which
cide for 10 amino acids.
5.1
Introduction
Aminoacyl-tRNA is transfer RNA carrying an amino acid; the covalent
linkage is between the NH2 group of the amino acid and either the 3′-
or 2′-OH group of the terminal base of the tRNA.
Aminoacyl-tRNA synthetases are enzymes responsible for covalently
linking amino acids to the 2′- or 3′-OH position of tRNA.
Anticodon is a trinucleotide sequence in tRNA which is complementary
to the codon in mRNA and enables the tRNA to place the appropriate
amino acid in response to the codon.
Loop is a single-stranded region at the end of a hairpin in RNA (or
single-stranded DNA); corresponds to the sequence between inverted
repeats in duplex DNA.
Stem is the base-paired segment of a hairpin.
5.2 Transfer RNA is the adapter
Figure 5.2 A tRNA has the
dual properties of an
adaptor that recognizes
both the amino acid and
codon,The 3 adenosine
is covalently linked to an
amino acid,The anticodon
base pairs with the codon
on mRNA.
5.2 Transfer RNA
is the adapter
Figure 5.3 The tRNA
cloverleaf has
invariant and semi-
invariant bases,and a
conserved set of base
pairing interactions.
5.2 Transfer RNA is
the adapter
Figure 5.4 Transfer
RNA folds into a
compact L-shaped
tertiary structure with
the amino acid at one
end and the anticodon at
the other end.
5.2 Transfer RNA
is the adapter
Figure 5.5 A space-filling
model shows that
tRNAPhe tertiary structure
is compact,The two views
of tRNA are rotated by 90o,
Photograph kindly
provided by S,H,Kim.
5.2 Transfer RNA
is the adapter
Figure 5.6 The meaning of tRNA is determined by
its anticodon and not by its amino acid.
5.2 Transfer RNA is the adapter
Figure 5.7 A
ribosome consists of
two subunits.
5.3 Messenger RNA is
translated by
ribosomes
Figure 5.8 A polyribosome consists of an mRNA being
translated simultaneously by several ribosomes moving in the
direction from 5 -3, Each ribosome has two tRNA
molecules,one carrying the nascent protein,thesexond
carrying the next amino acid to be added.
5.3 Messenger RNA is translated by ribosomes
Figure 5.9 A ribosome assembles from its subunits
on mRNA,translates the nucleotide triplets into
protein,and then dissociates from the mRNA.
5.3 Messenger RNA is translated by ribosomes
Figure 5.10 Protein synthesis occurs on polysomes,
Photograph kindly provided by Alex Rich.
5.3 Messenger RNA is translated by ribosomes
Figure 5.11
Messenger RNA is
translated by
ribosomes that cycle
through a pool.
5.3 Messenger
RNA is
translated by
ribosomes
Figure 5.12
Considering E,
coli in terms of its
macromolecular
components.
5.3 Messenger
RNA is
translated by
ribosomes
Coding region is a part of the gene that represents a protein
sequence.
Intercistronic region is the distance between the
termination codon of one gene and the initiation codon of
the next gene.
Leader of a protein is a short N-terminal sequence
responsible for passage into or through a membrane.
Trailer is a nontranslated sequence at the 3′ end of an
mRNA following the termination codon.
5.4 The life cycle of messenger RNA
Figure 5.13 Overview,
mRNA is transcribed,
translated,and degraded
simultaneously in bacteria.
5.4 The life cycle of
messenger RNA
Figure 5.14 Transcription units can be
visualized in bacteria,Photograph kindly
provided by Oscar Miller.
5.4 The life cycle of messenger RNA
Figure 5.15 Bacterial mRNA includes non-translated as well as
translated regions,Each coding region has its own initiation and
termination signals,A typical mRNA may have several coding
regions.
5.4 The life cycle of messenger RNA
Figure 5.16 Eukaryotic mRNA is modified
by addition of a cap to the 5 end and
poly(A) to the 3 end.
5.5 Translation of eukaryotic mRNA
Figure 5.17 Overview,
expression of mRNA in
animal cells requires
transcription,modification,
processing,
nucleocytoplasmic
transport,and translation.
5.5 Translation of
eukaryotic mRNA
Figure 5.17-2 Exogenous mRNAs can be translated by
cell-free systems or by injection into Xenopus oocytes.
5.5 Translation of eukaryotic mRNA
CAP (also known as CRP) is a
positive regulator protein activated by
cyclic AMP,It is needed for RNA
polymerase to initiate transcription of
certain (catabolite-sensitive) operons
of E,coli.
5.6 The 5 end of eukaryotic mRNA is capped
Figure 5.18 The cap
blocks the 5 end
of mRNA and may
be methylated at
several positions.
5.6 The 5 end of
eukaryotic mRNA is
capped
cDNA is a single-stranded DNA
complementary to an RNA,
synthesized from it by reverse
transcription in vitro.
5.7 The 3 terminus is polyadenylated
Figure 5.19
Poly(A)+ RNA
can be separated
from other RNAs
by fractionation on
Sepharose-
oligo(dT).
5.7 The 3 terminus
is polyadenylated
Degradosome is a complex of
bacterial enzymes,including
RNAases,a helicase,and enolase (a
glycolytic enzyme),which may be
involved in degrading mRNA.
5.8 Bacterial mRNA degradation
involves multiple enzymes
Figure 5.20 Degradation of
bacterial mRNA is a two
stage process,
Endonucleolytic cleavages
proceed 5 -3 behind the
ribosomes,The released
fragments are degraded by
exonucleases that move 3 -
5,
5.8 Bacterial mRNA
degradation
involves multiple
enzymes
Exosome is a complex
of several exonucleases
involved in degrading
RNA.
5.9 Yeast mRNA degradation
involves multiple activities
Figure 5.21
Degradation of
yeast mRNA
requires
deadenylation,
decapping,and
exonucleolysis.
5.9 Yeast mRNA
degradation involves
multiple activities
Figure 5.22 An
ARE in a 3
nontranslated
region initiates
degradation of
mRNA.
5.10 Sequence
elements may
destabilize mRNA
Figure 5.23 An
IRE in a 3
nontranslated
region controls
mRNA stability.
5.10 Sequence
elements may
destabilize mRNA
Surveillance systems check nucleic acids for
validity,The term is used in several different
contexts,One example is the system that
degrades mRNAs that have nonsense mutations,
Another is the set of systems that react to
damage in the double helix,The common
feature is that the system recognizes an invalid
sequence or structure and triggers a response.
5.11 Nonsense mutations trigger a
surveillance system
Figure 5.24
Nonsense
mutations may
cause mRNA to
be degraded.
5.11 Nonsense
mutations trigger a
surveillance system
1,Genetic information carried by DNA is expressed in two
stages,transcription of DNA into mRNA; and translation of
the mRNA into protein.
2,The adaptor that interprets the meaning of a codon is
transfer RNA,which has a compact L-shaped tertiary structure
3,The ribosome provides the apparatus that allows aminoacyl-
tRNAs to bind to their codons on mRNA.
4,The translational apparatus is not specific for tissue or
organism; an mRNA from one source can be translated by the
ribosomes and tRNAs from another source.
5.12 Summary
5,A typical mRNA contains both a nontranslated 5 leader
and 3 trailer as well as coding region(s).
6,A growing E,coli bacterium has ~20,000 ribosomes and
~200,000 tRNAs,mostly in the form of aminoacyl-tRNA.
7,Many ribosomes may translate a single mRNA
simultaneously,generating a polyribosome (or polysome).
8,Eukaryotic mRNA must be processed in the nucleus
before it is transported to the cytoplasm for translation.
9,Yeast mRNA is degraded by multiple pathways.
Eukaryotic mRNAs are usually stable for several hours.
5.12 Summary
Messenger
RNA
? 5.1 Introduction
? 5.2 Transfer RNA is the adapter
? 5.3 Messenger RNA is translated by ribosomes
? 5.4 The life cycle of bacterial messenger RNA
? 5.5 Translation of eukaryotic mRNA
? 5.6 The 5? end of eukaryotic mRNA is capped
? 5.7 The 3? terminus is polyadenylated
? 5.8 Bacterial mRNA degradation involves multiple enzymes
? 5.9 mRNA degradation involves multiple activities
? 5.10 Sequence elements may destabilize mRNA
? 5.11 Nonsense mutations trigger a surveillance system
Coding region is a part of the gene that represents a
protein sequence.
Coding strand of DNA has the same sequence as
mRNA.
template strand of double-stranded DNA is the one that
is used to specify the sequence of a complementary
single strand of RNA,(The non-template strand is
identical in sequence to the RNA product.)
Transcription is synthesis of RNA on a DNA template.
Translation is synthesis of protein on the mRNA
template.
5.1 Introduction
Figure 5.1 Transcription
generates an RNA which is
complementary to the DNA
template strand and has the
same sequence as the DNA
coding strand,Translation
reads each triplet of bases
into one amino acid,Three
turns of the DNA double
helix contain 30 bp,which
cide for 10 amino acids.
5.1
Introduction
Aminoacyl-tRNA is transfer RNA carrying an amino acid; the covalent
linkage is between the NH2 group of the amino acid and either the 3′-
or 2′-OH group of the terminal base of the tRNA.
Aminoacyl-tRNA synthetases are enzymes responsible for covalently
linking amino acids to the 2′- or 3′-OH position of tRNA.
Anticodon is a trinucleotide sequence in tRNA which is complementary
to the codon in mRNA and enables the tRNA to place the appropriate
amino acid in response to the codon.
Loop is a single-stranded region at the end of a hairpin in RNA (or
single-stranded DNA); corresponds to the sequence between inverted
repeats in duplex DNA.
Stem is the base-paired segment of a hairpin.
5.2 Transfer RNA is the adapter
Figure 5.2 A tRNA has the
dual properties of an
adaptor that recognizes
both the amino acid and
codon,The 3 adenosine
is covalently linked to an
amino acid,The anticodon
base pairs with the codon
on mRNA.
5.2 Transfer RNA
is the adapter
Figure 5.3 The tRNA
cloverleaf has
invariant and semi-
invariant bases,and a
conserved set of base
pairing interactions.
5.2 Transfer RNA is
the adapter
Figure 5.4 Transfer
RNA folds into a
compact L-shaped
tertiary structure with
the amino acid at one
end and the anticodon at
the other end.
5.2 Transfer RNA
is the adapter
Figure 5.5 A space-filling
model shows that
tRNAPhe tertiary structure
is compact,The two views
of tRNA are rotated by 90o,
Photograph kindly
provided by S,H,Kim.
5.2 Transfer RNA
is the adapter
Figure 5.6 The meaning of tRNA is determined by
its anticodon and not by its amino acid.
5.2 Transfer RNA is the adapter
Figure 5.7 A
ribosome consists of
two subunits.
5.3 Messenger RNA is
translated by
ribosomes
Figure 5.8 A polyribosome consists of an mRNA being
translated simultaneously by several ribosomes moving in the
direction from 5 -3, Each ribosome has two tRNA
molecules,one carrying the nascent protein,thesexond
carrying the next amino acid to be added.
5.3 Messenger RNA is translated by ribosomes
Figure 5.9 A ribosome assembles from its subunits
on mRNA,translates the nucleotide triplets into
protein,and then dissociates from the mRNA.
5.3 Messenger RNA is translated by ribosomes
Figure 5.10 Protein synthesis occurs on polysomes,
Photograph kindly provided by Alex Rich.
5.3 Messenger RNA is translated by ribosomes
Figure 5.11
Messenger RNA is
translated by
ribosomes that cycle
through a pool.
5.3 Messenger
RNA is
translated by
ribosomes
Figure 5.12
Considering E,
coli in terms of its
macromolecular
components.
5.3 Messenger
RNA is
translated by
ribosomes
Coding region is a part of the gene that represents a protein
sequence.
Intercistronic region is the distance between the
termination codon of one gene and the initiation codon of
the next gene.
Leader of a protein is a short N-terminal sequence
responsible for passage into or through a membrane.
Trailer is a nontranslated sequence at the 3′ end of an
mRNA following the termination codon.
5.4 The life cycle of messenger RNA
Figure 5.13 Overview,
mRNA is transcribed,
translated,and degraded
simultaneously in bacteria.
5.4 The life cycle of
messenger RNA
Figure 5.14 Transcription units can be
visualized in bacteria,Photograph kindly
provided by Oscar Miller.
5.4 The life cycle of messenger RNA
Figure 5.15 Bacterial mRNA includes non-translated as well as
translated regions,Each coding region has its own initiation and
termination signals,A typical mRNA may have several coding
regions.
5.4 The life cycle of messenger RNA
Figure 5.16 Eukaryotic mRNA is modified
by addition of a cap to the 5 end and
poly(A) to the 3 end.
5.5 Translation of eukaryotic mRNA
Figure 5.17 Overview,
expression of mRNA in
animal cells requires
transcription,modification,
processing,
nucleocytoplasmic
transport,and translation.
5.5 Translation of
eukaryotic mRNA
Figure 5.17-2 Exogenous mRNAs can be translated by
cell-free systems or by injection into Xenopus oocytes.
5.5 Translation of eukaryotic mRNA
CAP (also known as CRP) is a
positive regulator protein activated by
cyclic AMP,It is needed for RNA
polymerase to initiate transcription of
certain (catabolite-sensitive) operons
of E,coli.
5.6 The 5 end of eukaryotic mRNA is capped
Figure 5.18 The cap
blocks the 5 end
of mRNA and may
be methylated at
several positions.
5.6 The 5 end of
eukaryotic mRNA is
capped
cDNA is a single-stranded DNA
complementary to an RNA,
synthesized from it by reverse
transcription in vitro.
5.7 The 3 terminus is polyadenylated
Figure 5.19
Poly(A)+ RNA
can be separated
from other RNAs
by fractionation on
Sepharose-
oligo(dT).
5.7 The 3 terminus
is polyadenylated
Degradosome is a complex of
bacterial enzymes,including
RNAases,a helicase,and enolase (a
glycolytic enzyme),which may be
involved in degrading mRNA.
5.8 Bacterial mRNA degradation
involves multiple enzymes
Figure 5.20 Degradation of
bacterial mRNA is a two
stage process,
Endonucleolytic cleavages
proceed 5 -3 behind the
ribosomes,The released
fragments are degraded by
exonucleases that move 3 -
5,
5.8 Bacterial mRNA
degradation
involves multiple
enzymes
Exosome is a complex
of several exonucleases
involved in degrading
RNA.
5.9 Yeast mRNA degradation
involves multiple activities
Figure 5.21
Degradation of
yeast mRNA
requires
deadenylation,
decapping,and
exonucleolysis.
5.9 Yeast mRNA
degradation involves
multiple activities
Figure 5.22 An
ARE in a 3
nontranslated
region initiates
degradation of
mRNA.
5.10 Sequence
elements may
destabilize mRNA
Figure 5.23 An
IRE in a 3
nontranslated
region controls
mRNA stability.
5.10 Sequence
elements may
destabilize mRNA
Surveillance systems check nucleic acids for
validity,The term is used in several different
contexts,One example is the system that
degrades mRNAs that have nonsense mutations,
Another is the set of systems that react to
damage in the double helix,The common
feature is that the system recognizes an invalid
sequence or structure and triggers a response.
5.11 Nonsense mutations trigger a
surveillance system
Figure 5.24
Nonsense
mutations may
cause mRNA to
be degraded.
5.11 Nonsense
mutations trigger a
surveillance system
1,Genetic information carried by DNA is expressed in two
stages,transcription of DNA into mRNA; and translation of
the mRNA into protein.
2,The adaptor that interprets the meaning of a codon is
transfer RNA,which has a compact L-shaped tertiary structure
3,The ribosome provides the apparatus that allows aminoacyl-
tRNAs to bind to their codons on mRNA.
4,The translational apparatus is not specific for tissue or
organism; an mRNA from one source can be translated by the
ribosomes and tRNAs from another source.
5.12 Summary
5,A typical mRNA contains both a nontranslated 5 leader
and 3 trailer as well as coding region(s).
6,A growing E,coli bacterium has ~20,000 ribosomes and
~200,000 tRNAs,mostly in the form of aminoacyl-tRNA.
7,Many ribosomes may translate a single mRNA
simultaneously,generating a polyribosome (or polysome).
8,Eukaryotic mRNA must be processed in the nucleus
before it is transported to the cytoplasm for translation.
9,Yeast mRNA is degraded by multiple pathways.
Eukaryotic mRNAs are usually stable for several hours.
5.12 Summary
