Transcript THE CODE IS DEGENERATE

Li Xiaoling
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Content
Chapter 1 Introduction
Chapter 2 The Structures of DNA and RNA
Chapter 3 DNA Replication
Chapter 4 DNA Mutation and Repair
Chapter 5 RNA Transcription
Chapter 6 RNA Splicing
Chapter 7 Translation
Chapter 8 The Genetic code
Chapter 9 Regulation in prokaryotes
Chapter 10 Regulation in Eukaryotes
2016/4/4
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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
3/22/05
EXPRESSION OF THE
GENOME
Ch 5 : Transcription
Ch 6 : RNA Splicing
Ch 7 : Translation
Ch 8 : The Genetic code
4/3/05
The Central Dogma
Transcription
DNA
Replication
Protein
RNA
Translation
1. Genetic information transfer
from polynucleotide chain
into polypeptide chain.
2. Take place in ribosomes.
3. tRNAs recognize codons.
CHAPTER 8 The Genetic Code
Topic 1: THE CODE IS
DEGENERATE
Codon: degenerate
Anticodon: wobble
TABLE 8-1
The Genetic Code
Many amino
acids are
specified by
more than
one codondegeneracy
(简并性).
Codons
specifying
the same
amino acid
are called
synonyms
(同义密码子).
CODING ROLE #1
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.
CUG
CUC
Figure 8-1 Codon-anticodon
pairing of two tRNA Leu moleculars
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.
The Code Is Degenerate
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.
CODING ROLE #2
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
The Code Is Degenerate
(反密码子具有摇摆性)
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
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 8-2 Pairing Combinations
with the Wobble Concept
Base in 5’ Anticodon
G
C
A
U
I
Base in 3’ Codon
U or C
G
U
A or G
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
The ribose-ribose
distances for the wobble
pairs are close to those of
A:U or G:C base pairs
Figure 8-2
Wobble base pairing
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.

The
adjacent
base
The adjacent base is always a
bulky modified purine residue.
Figure 8-3 Structure of yeast tRNA(Phe)
The Code Is Degenerate
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).
The Code Is Degenerate
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
Stimulation of Amino Acid
Incorporation by Synthetic mRNAs
The Code Is Degenerate
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
Figure 8-4 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.
The Code Is Degenerate
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
Such experiment can
determine the composition of
the codons, but not the order
of the three nucleotides.
See Table 8-3 on Page 467
Transfer RNA Binding to Defined
Trinucleotide Codons (1964)
The Code Is Degenerate
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 aminoacyl-tRNA attachment.
The Code Is Degenerate
Codon Assignments from
Repeating Copolymers
Organic chemical and
enzymatic techniques were
used to prepare synthetic
polyribonucleotides with
known repeating sequences.
Figure 8-5 Preparing oligo-ribonucleotides
Table 8-5
Amino Acids
Codons
Codon
copolymer
Recognized Incorporated or Assignment
Polypeptide Made
(CU)”
(UG)”
(AC)”
(AG)”
(AUC)”
CUC|UCU|CUC…
UGU|GUG|UGU…
ACA|CAC|ACA…
AGA|GAG|AGA…
AUC|AUC|AUC…
Leucine
5’-CUC-3’
Serine
UCU
Cystine
UGU
Valine
GUG
Threonine
ACA
Histidine
CAC
Arginine
AGA
Glutamine
GAG
Polyisoleucine
5’-AUC-3’
CHAPTER 8 The Genetic Code
Topic 2: THREE
RULES GOVERN THE
GENETIC CODE
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 Rules Govern the Genetic Code
Three Kinds of Point Mutations
Alter the Genetic Code
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.
Three Rules Govern the Genetic Code
Genetic Proof that the Code Is
Read in Units of Three
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.
CHAPTER 8 The Genetic Code
Topic 3:
SUPPRESSOR
MUTATIONS CAN
RESIDE IN THE SAME
OR A DIFFERENT
GENE
4/22/05
Reverse the harmful mutations
by a second genetic change


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
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 8-6 Suppression of frameshift mutations
Intergenic Suppression Involves
Mutant tRNAs
Suppressor mutations
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 8-7 a
Figure 15-7 a
Figure 8-7 b
Nonsense Suppressors also Read
Normal Termination Signals (OOPs)
Suppressor mutations
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??.
CHAPTER 8 The Genetic Code
Topic 4:
THE CODE IS NEARLY
UNIVERSAL
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 8-6 Genetic Code of Mammalian Mitochondria
Key points of the chapter
1. “The genetic code is degenerate” What does
it mean? What are the benefits?
2. What is the wobble concept? Is there
structural evidence? How the wobble in the
anticodon affect the number of tRNAs to
recognize the 61 codons?
3. What are the three roles governing the
genetic code? What are the mutations
altering genetic code?
4. What are suppressor mutations? (种类)
5. What are the benefits of the code
universality?