Welcome Each of
You to My
Molecular Biology
Class
Molecular Biology of the Gene,
5/E --- Watson et al,(2004)
Part I,Chemistry and Genetics
Part II,Maintenance of the Genome
Part III,Expression of the Genome
Part IV,Regulation
Part V,Methods
3/22/05
Part III,Expression of the Genome
Ch 12,Mechanisms of
Transcription
Ch 13,RNA Splicing
Ch 14,Translation
Ch 15,The Genetic Code
CHAPTER 15
The Genetic Code
?Molecular Biology Course
DNA RNA Protein
Replication
Transcription
Translation
The Central Dogma
1,Genetic information transfer
from polynucleotide chain
into polypeptide chain.
2,Take place in ribosomes.
3,tRNAs recognize codons.
Topic 1,THE CODE IS
DEGENERATE
CHAPTER 15 The Genetic Code
4/22/05
Many amino
acids are
specified by
more than
one codon-
degeneracy
(简并性 ).
Codons
specifying
the same
amino acid
are called
synonyms
(同义密码子 ).
TABLE 15-1
The Genetic Code
Detail 1,Code Degeneracy
1,Often,when the first two nucleotides
are identical,the third nucleotide can
be either C or U without changing the
code,A and G at the third position are
interchangeable as well,
2,Transition in the third position of a
codon specifies a same amino acid,
Transversion in this position changes
the amino acid about half the time.
Figure 15-1 Codon-anticodon
pairing of two tRNA Leu moleculars
CUG CUC
Code degeneracy explains
how there can be great
variation in the AT/GC ratios
in the DNA of various
organisms without large
changes in the proportion of
amino acids in their proteins.
Perceiving Order in the
Makeup of the Code
1.The genetic code evolved in
such a way as to minimize the
deleterious effects of
mutations,
2.Code degeneracy may serve as
a safety mechanism to
minimize errors in the reading
of codons.
Th
e Co
de
Is
Deg
en
er
ate
Detail 2,Code Degeneracy
1.The second position of a codon:
? Pyrimidines-hydrophobic amino
acids
? Purines-polar amino acids
2.If the first two positions are both
occupied by G or C,each of the four
nucleotides in the third position
specifies the same amino acid,
Wobble in the Anticodon
Question,Is there a specific tRNA for
every codon? (If it was true,at least
61 different tRNAs would exist.)
The answer is NO
? Some tRNA could recognize several
different codons
? Inosine is present in the anticodon
loop as a fifth base
Th
e Co
de
Is
Deg
en
er
ate
Inosine
inosine adenine
Inosine arises through enzymatic
modification of adenine
Wobble Concept
In 1966,Francis Crick devised
the wobble concept,It states
that 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 more than one bases
located at the 3’ end of a codon.
Table 15-2 Pairing Combinations
with the Wobble Concept
Base in 5’ Anticodon Base in 3’ Codon
G U or C
C G
A U
U A or G
I A,U,or C
The Wobble Rules
?The pairings permitted are
those give ribose-ribose
distances close to that of the
standard A:U or G:C base
pairs.
?The ribose-ribose distances:
? Purine-purine,too long
? Pyrimidine-pyrimidine,too short
Figure 15-2
Wobble base pairing
The ribose-ribose
distances for the wobble
pairs are close to those of
A:U or G:C base pairs
Critical Thinking
The wobble concept
predicted that at least
three tRNAs exist for the
six serine codons (UCU,
UCC,UCA,UCG,AGU,and
AGC),Why?
Why wobble is allowed at the 5’
anticodon
? The 3-D structure of tRNA shows that
the stacking interactions between the
flat surfaces of the 3 anticodon bases +
2 followed bases position the first (5’)
anticodon base at the end of the stack,
thus less restricted in its movements.
? The 3’ base appears in the middle of the
stack,resulting in the restriction of its
movements.
Figure 15-3 Structure of yeast tRNA(Phe)
The
adjacent
base
The adjacent base is always a
bulky modified purine residue.
Three Codons Direct Chain
Termination
?Three codons,UAA,UAG,and
UGA signify chain termination.
?They are not read by tRNAs but
by proteins called release factors
(RF1 and RF2 in bacteria and
eRF1 in eukaryotes).
Th
e Co
de
Is
Deg
en
er
ate
How the Code Was Cracked
(解开 )
? See Chapter 2,Page 35:
Establishing the Genetic Code
? The use of artificial mRNAs and the
availability of cell-free systems for
carrying out protein synthesis
began to make it possible to crack
the code
Th
e Co
de
Is
Deg
en
er
ate
Stimulation of Amino Acid
Incorporation by Synthetic mRNAs
Extracts from E,coli cells can incorporate
amino acids into proteins.
After several minutes the synthesis came
to a stop because the degradation of
mRNA,The addition of fresh mRNA to
extracts caused an immediate
resumption of synthesis.
This led the scientist an opportunity to
elucidate the nature of the code using
synthetic RNA
Th
e Co
de
Is
Deg
en
er
ate
Figure 15-4 Polynucleotide phosphorylase reaction
How the RNA is synthesized?
[XMP]n + XDP = [XMP]n+1 + P
Experimental Results,
?UUU codes for phenylalanine.
?CCC codes for proline.
?AAA codes for lysine.
?The guanine residues in poly-G
firmly hydrogen bond to each
other and form multistranded
triple helices that do not bind to
ribosomes.
Mixed Copolymers Allowed
Additional Codon Assignments
? Poly-AC contain 8 codons,CCC,CCA,
CAC,ACC,CAA,ACA,AAC,and AAA.
? They code for Asp,Glu,His,Thr & Pro
(CCC),Lys (AAA),
The proportions of the 8 codons
incorporated into polypeptide
products depend on the A/C ratio
Th
e Co
de
Is
Deg
en
er
ate
Such experiment can
determine the composition of
the codons,but not the order
of the three nucleotides.
See Table 15-3 on Page 467
Transfer RNA Binding to Defined
Trinucleotide Codons (1964)T
he
Co
de
Is
Deg
en
er
ate
?A method to order the
nucleotides within some of the
codons.
?Specific amino-acyl-tRNA can
bind to ribosome-mRNA complexes.
?The addition of trinucleotide
results in corresponding amino-
acyl-tRNA attachment.
Codon Assignments from
Repeating CopolymersTh
e Co
de
Is
Deg
en
er
ate
?Organic chemical and
enzymatic techniques were
used to prepare synthetic
polyribonucleotides with
known repeating sequences.
Figure 15-5 Preparing oligo-ribonucleotides
Table 15-5
copolymer Codons Recognized Amino Acids Incorporated or
Polypeptide Made
Codon
Assignment
(CU)” CUC|UCU|CUC… Leucine 5’ -CUC-3’
Serine UCU
(UG)” UGU|GUG|UGU… Cystine UGU
Valine GUG
(AC)” ACA|CAC|ACA… Threonine ACA
Histidine CAC
(AG)” AGA|GAG|AGA… Arginine AGA
Glutamine GAG
(AUC)” AUC|AUC|AUC… Polyisoleucine 5’ -AUC-3’
Topic 2,THREE
RULES GOVERN THE
GENETIC CODE
CHAPTER 15 The Genetic Code
4/22/05
Three Rules
?Codons are read in a 5’ to 3’
direction.
?Codons are nonoverlapping and
the message contains no gaps.
?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
Th
ree
Ru
les
Go
ve
rn
the
Ge
ne
tic
Co
de
1,Missense mutation,An
alternation that changes a codon
specific for one amino acid to a
codon specific for another amino
acid.
2,Nonsense or stop mutation,An
alternation causing a change to a
chain-termination codon.
3,Frameshift mutation:
Insertions or deletions of
one or a small number of
base pairs that alter the
reading frame.
Genetic Proof that the Code Is
Read in Units of Three
Th
ree
Ru
les
Go
ve
rn
the
Ge
ne
tic
Co
de
?A classic experiment involving
bacteriophage T4
?Because the gene could
tolerate three insertions but not
one or two,the genetic code
must be read in units of three.
Topic 3,
SUPPRESSOR
MUTATIONS CAN
RESIDE IN THE SAME
OR A DIFFERENT
GENE
CHAPTER 15 The Genetic Code
4/22/05
? Reverse (back) mutations,change
an altered nucleotide sequence
back to its original arrangement.
? Suppressor mutations,suppress
the change due to mutation at site
A by producing an additional
genetic change at site B.
(1) Intragenic suppression
(2) Intergenic suppression
Reverse the harmful mutations
by a second genetic change
?Suppressor genes,genes that
cause suppression of
mutations in other genes.
?Suppressor mutations work
by producing good (or
partially good) copies of the
protein that are made inactive
by the original harmful
mutation.
Figure 15-6 Suppression of frameshift mutations
Intergenic Suppression Involves
Mutant tRNAs
Su
pp
re
ss
or
m
ut
at
io
ns
?Mutant tRNA genes suppress
the effects of nonsense
mutations in protein-coding
genes,
?They act by reading a stop
codon as if it were a signal for a
specific amino acid.
Figure 15-7 a
Figure 15-7 a
Figure 15-7 b
Nonsense Suppressors also Read
Normal Termination Signals (OOPs)
Su
pp
re
ss
or
m
ut
at
io
ns
?The act of nonsense suppression is
a competition between the
suppressor tRNA and the release
factor.
?In E,coli,Suppression of UAG
codons is efficient,and suppression
of UAA codon average is inefficient,
Why.
Topic 4,
THE CODE IS NEARLY
UNIVERSAL
CHAPTER 15 The Genetic Code
4/22/05
The results of large-scale
sequencing of genomes have
confirmed the universality of
the genetic code.
Benefits of the universal codes
(1)Allow us to directly compare the
protein coding sequences among all
organisms.
(2) Make it possible to express
cloned copies of genes encoding
useful protein in different host
organism,Example,Human insulin
ecpression in bacteria)
?However,in certain subcellular
organelles,the genetic code is
slightly different from the
standard code.
?Mitochondrial tRNAs are unusual in
the way that they decode
mitochondrial messages.
?Only 22 tRNAs are present in
mammalian mitochondria,The U in
the 5’ wobble position of a tRNA is
capable of recognizing all four
bases in the 3’ of the codon.
Table 15-6 Genetic Code of Mammalian Mitochondria
1.“The genetic code is degenerate” What
does it mean? What’s the benefits?
What’s about the anticodon recognition?
How the code was discovered?
2,What are the three roles governing the
genetic code? What are the mutations
altering genetic code?
3,What are suppressor mutations? (种类 )
4,What are the benefits of the code
universality? What’s about the
mitochondrial codes and tRNAs?
Key points of the chapter
学时分配和教学日历
Introduction,1.5学时
Part I,Chemistry and Genetics (chapter 1-5,
第 1周,3.5 学时）
Part II,Maintenance of the Genome
(chapter 6-11,第 2-6周,25 学时）
Part III,Expression of the Genome
(chapter 12-15,第 7-9,11周,15 学时 (出差占 2)
Part IV,Regulation
(chapter 16-19,第 11-12,14-16周,20学时）
Part V,Methods
(chapter 20-21,第 16-17周,8 学时）
Total 73 学时
You to My
Molecular Biology
Class
Molecular Biology of the Gene,
5/E --- Watson et al,(2004)
Part I,Chemistry and Genetics
Part II,Maintenance of the Genome
Part III,Expression of the Genome
Part IV,Regulation
Part V,Methods
3/22/05
Part III,Expression of the Genome
Ch 12,Mechanisms of
Transcription
Ch 13,RNA Splicing
Ch 14,Translation
Ch 15,The Genetic Code
CHAPTER 15
The Genetic Code
?Molecular Biology Course
DNA RNA Protein
Replication
Transcription
Translation
The Central Dogma
1,Genetic information transfer
from polynucleotide chain
into polypeptide chain.
2,Take place in ribosomes.
3,tRNAs recognize codons.
Topic 1,THE CODE IS
DEGENERATE
CHAPTER 15 The Genetic Code
4/22/05
Many amino
acids are
specified by
more than
one codon-
degeneracy
(简并性 ).
Codons
specifying
the same
amino acid
are called
synonyms
(同义密码子 ).
TABLE 15-1
The Genetic Code
Detail 1,Code Degeneracy
1,Often,when the first two nucleotides
are identical,the third nucleotide can
be either C or U without changing the
code,A and G at the third position are
interchangeable as well,
2,Transition in the third position of a
codon specifies a same amino acid,
Transversion in this position changes
the amino acid about half the time.
Figure 15-1 Codon-anticodon
pairing of two tRNA Leu moleculars
CUG CUC
Code degeneracy explains
how there can be great
variation in the AT/GC ratios
in the DNA of various
organisms without large
changes in the proportion of
amino acids in their proteins.
Perceiving Order in the
Makeup of the Code
1.The genetic code evolved in
such a way as to minimize the
deleterious effects of
mutations,
2.Code degeneracy may serve as
a safety mechanism to
minimize errors in the reading
of codons.
Th
e Co
de
Is
Deg
en
er
ate
Detail 2,Code Degeneracy
1.The second position of a codon:
? Pyrimidines-hydrophobic amino
acids
? Purines-polar amino acids
2.If the first two positions are both
occupied by G or C,each of the four
nucleotides in the third position
specifies the same amino acid,
Wobble in the Anticodon
Question,Is there a specific tRNA for
every codon? (If it was true,at least
61 different tRNAs would exist.)
The answer is NO
? Some tRNA could recognize several
different codons
? Inosine is present in the anticodon
loop as a fifth base
Th
e Co
de
Is
Deg
en
er
ate
Inosine
inosine adenine
Inosine arises through enzymatic
modification of adenine
Wobble Concept
In 1966,Francis Crick devised
the wobble concept,It states
that 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 more than one bases
located at the 3’ end of a codon.
Table 15-2 Pairing Combinations
with the Wobble Concept
Base in 5’ Anticodon Base in 3’ Codon
G U or C
C G
A U
U A or G
I A,U,or C
The Wobble Rules
?The pairings permitted are
those give ribose-ribose
distances close to that of the
standard A:U or G:C base
pairs.
?The ribose-ribose distances:
? Purine-purine,too long
? Pyrimidine-pyrimidine,too short
Figure 15-2
Wobble base pairing
The ribose-ribose
distances for the wobble
pairs are close to those of
A:U or G:C base pairs
Critical Thinking
The wobble concept
predicted that at least
three tRNAs exist for the
six serine codons (UCU,
UCC,UCA,UCG,AGU,and
AGC),Why?
Why wobble is allowed at the 5’
anticodon
? The 3-D structure of tRNA shows that
the stacking interactions between the
flat surfaces of the 3 anticodon bases +
2 followed bases position the first (5’)
anticodon base at the end of the stack,
thus less restricted in its movements.
? The 3’ base appears in the middle of the
stack,resulting in the restriction of its
movements.
Figure 15-3 Structure of yeast tRNA(Phe)
The
adjacent
base
The adjacent base is always a
bulky modified purine residue.
Three Codons Direct Chain
Termination
?Three codons,UAA,UAG,and
UGA signify chain termination.
?They are not read by tRNAs but
by proteins called release factors
(RF1 and RF2 in bacteria and
eRF1 in eukaryotes).
Th
e Co
de
Is
Deg
en
er
ate
How the Code Was Cracked
(解开 )
? See Chapter 2,Page 35:
Establishing the Genetic Code
? The use of artificial mRNAs and the
availability of cell-free systems for
carrying out protein synthesis
began to make it possible to crack
the code
Th
e Co
de
Is
Deg
en
er
ate
Stimulation of Amino Acid
Incorporation by Synthetic mRNAs
Extracts from E,coli cells can incorporate
amino acids into proteins.
After several minutes the synthesis came
to a stop because the degradation of
mRNA,The addition of fresh mRNA to
extracts caused an immediate
resumption of synthesis.
This led the scientist an opportunity to
elucidate the nature of the code using
synthetic RNA
Th
e Co
de
Is
Deg
en
er
ate
Figure 15-4 Polynucleotide phosphorylase reaction
How the RNA is synthesized?
[XMP]n + XDP = [XMP]n+1 + P
Experimental Results,
?UUU codes for phenylalanine.
?CCC codes for proline.
?AAA codes for lysine.
?The guanine residues in poly-G
firmly hydrogen bond to each
other and form multistranded
triple helices that do not bind to
ribosomes.
Mixed Copolymers Allowed
Additional Codon Assignments
? Poly-AC contain 8 codons,CCC,CCA,
CAC,ACC,CAA,ACA,AAC,and AAA.
? They code for Asp,Glu,His,Thr & Pro
(CCC),Lys (AAA),
The proportions of the 8 codons
incorporated into polypeptide
products depend on the A/C ratio
Th
e Co
de
Is
Deg
en
er
ate
Such experiment can
determine the composition of
the codons,but not the order
of the three nucleotides.
See Table 15-3 on Page 467
Transfer RNA Binding to Defined
Trinucleotide Codons (1964)T
he
Co
de
Is
Deg
en
er
ate
?A method to order the
nucleotides within some of the
codons.
?Specific amino-acyl-tRNA can
bind to ribosome-mRNA complexes.
?The addition of trinucleotide
results in corresponding amino-
acyl-tRNA attachment.
Codon Assignments from
Repeating CopolymersTh
e Co
de
Is
Deg
en
er
ate
?Organic chemical and
enzymatic techniques were
used to prepare synthetic
polyribonucleotides with
known repeating sequences.
Figure 15-5 Preparing oligo-ribonucleotides
Table 15-5
copolymer Codons Recognized Amino Acids Incorporated or
Polypeptide Made
Codon
Assignment
(CU)” CUC|UCU|CUC… Leucine 5’ -CUC-3’
Serine UCU
(UG)” UGU|GUG|UGU… Cystine UGU
Valine GUG
(AC)” ACA|CAC|ACA… Threonine ACA
Histidine CAC
(AG)” AGA|GAG|AGA… Arginine AGA
Glutamine GAG
(AUC)” AUC|AUC|AUC… Polyisoleucine 5’ -AUC-3’
Topic 2,THREE
RULES GOVERN THE
GENETIC CODE
CHAPTER 15 The Genetic Code
4/22/05
Three Rules
?Codons are read in a 5’ to 3’
direction.
?Codons are nonoverlapping and
the message contains no gaps.
?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
Th
ree
Ru
les
Go
ve
rn
the
Ge
ne
tic
Co
de
1,Missense mutation,An
alternation that changes a codon
specific for one amino acid to a
codon specific for another amino
acid.
2,Nonsense or stop mutation,An
alternation causing a change to a
chain-termination codon.
3,Frameshift mutation:
Insertions or deletions of
one or a small number of
base pairs that alter the
reading frame.
Genetic Proof that the Code Is
Read in Units of Three
Th
ree
Ru
les
Go
ve
rn
the
Ge
ne
tic
Co
de
?A classic experiment involving
bacteriophage T4
?Because the gene could
tolerate three insertions but not
one or two,the genetic code
must be read in units of three.
Topic 3,
SUPPRESSOR
MUTATIONS CAN
RESIDE IN THE SAME
OR A DIFFERENT
GENE
CHAPTER 15 The Genetic Code
4/22/05
? Reverse (back) mutations,change
an altered nucleotide sequence
back to its original arrangement.
? Suppressor mutations,suppress
the change due to mutation at site
A by producing an additional
genetic change at site B.
(1) Intragenic suppression
(2) Intergenic suppression
Reverse the harmful mutations
by a second genetic change
?Suppressor genes,genes that
cause suppression of
mutations in other genes.
?Suppressor mutations work
by producing good (or
partially good) copies of the
protein that are made inactive
by the original harmful
mutation.
Figure 15-6 Suppression of frameshift mutations
Intergenic Suppression Involves
Mutant tRNAs
Su
pp
re
ss
or
m
ut
at
io
ns
?Mutant tRNA genes suppress
the effects of nonsense
mutations in protein-coding
genes,
?They act by reading a stop
codon as if it were a signal for a
specific amino acid.
Figure 15-7 a
Figure 15-7 a
Figure 15-7 b
Nonsense Suppressors also Read
Normal Termination Signals (OOPs)
Su
pp
re
ss
or
m
ut
at
io
ns
?The act of nonsense suppression is
a competition between the
suppressor tRNA and the release
factor.
?In E,coli,Suppression of UAG
codons is efficient,and suppression
of UAA codon average is inefficient,
Why.
Topic 4,
THE CODE IS NEARLY
UNIVERSAL
CHAPTER 15 The Genetic Code
4/22/05
The results of large-scale
sequencing of genomes have
confirmed the universality of
the genetic code.
Benefits of the universal codes
(1)Allow us to directly compare the
protein coding sequences among all
organisms.
(2) Make it possible to express
cloned copies of genes encoding
useful protein in different host
organism,Example,Human insulin
ecpression in bacteria)
?However,in certain subcellular
organelles,the genetic code is
slightly different from the
standard code.
?Mitochondrial tRNAs are unusual in
the way that they decode
mitochondrial messages.
?Only 22 tRNAs are present in
mammalian mitochondria,The U in
the 5’ wobble position of a tRNA is
capable of recognizing all four
bases in the 3’ of the codon.
Table 15-6 Genetic Code of Mammalian Mitochondria
1.“The genetic code is degenerate” What
does it mean? What’s the benefits?
What’s about the anticodon recognition?
How the code was discovered?
2,What are the three roles governing the
genetic code? What are the mutations
altering genetic code?
3,What are suppressor mutations? (种类 )
4,What are the benefits of the code
universality? What’s about the
mitochondrial codes and tRNAs?
Key points of the chapter
学时分配和教学日历
Introduction,1.5学时
Part I,Chemistry and Genetics (chapter 1-5,
第 1周,3.5 学时）
Part II,Maintenance of the Genome
(chapter 6-11,第 2-6周,25 学时）
Part III,Expression of the Genome
(chapter 12-15,第 7-9,11周,15 学时 (出差占 2)
Part IV,Regulation
(chapter 16-19,第 11-12,14-16周,20学时）
Part V,Methods
(chapter 20-21,第 16-17周,8 学时）
Total 73 学时
