The Genetic Code

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The Genetic Code

• Chapter 15
• ??? 200431060050

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The central dogma
Translation key words tRNA(transfer RNAs) the
special adaptor molecules mediate the translation
of genetic Codons Three consecutive nucleotides
The total number is 64 while the amino acids
number is 22
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Outline

• The Code Is Degenerate
• Three Rules Govern the Genetic Code
• Suppressor Mutations Can Reside in the Same or a
  Different Gene
• The Code is Nearly Universal

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Topic 1 The Code Is Degenerate

• concepts
• Many amino acides are specified by more than
  one codon, the phenomenon called degeneracy.
• codons specifying the same amino acid are
  synonyms

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The Code Is Degenerate

• 1 When the first two nucletides are identical,
  the third nucleotide can be either cytosine or
  uracil and the codon will still code for the same
  amino acid, C and U,A and G can be
  interchangeable
• Not all degeneracy is based on equivalence of the
  first two nucleotides
• leucine UUA?UUG?CUU?CUC?CUA?CUG
• 3 There can be great variation in the AT/GC
  ratios in the DNA of various organisms without
  correspondingly large changes in the relative
  proportion of amino acids in their proteins

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Perceiving Order in the Makeup of the Code

• 1 The code evolved in such a way as to minimize
  the deleterious effects of mutations
• Examples a Mutation in the first position
  of a codon will often give a similar amino acid.
• bCodons with pyrimidines in the
  second position specify mostly hydrophobic
  amino acids,with purines in the second position
  correspond mostly to polar amino acids.
• cChange in the third position
  rarely will a different amino acid be
  specified,even a
  transversion mutation.
• 
  

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Perceiving Order in the Makeup of the Code

• 2 degeneracy may function as a safety mechanism
  to minimize errors in reading of such condons.
• Whenever the first two positions of a codon are
  both occupied by G or C, each of the four
  nucleotides in the third position specifies the
  same amino acid.
• On the other hand, Whenever the first two
  positions of the codon are both occupied by A or
  U, the identity of the third nucleotide does make
  a difference.
• Since GC pairs are stronger than AU ones

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Wobble in the Anticodon

• Problem If there is a specific tRNA for every
  codon , at least 61different tRNAs would exist.)
  while the truth is
• Some tRNA could recognize several different
  codons
• Inosine is found in the anticodon loop as a fifth
  base

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Wobble in the Anticodon

• In 1966, Francis Crick
• Wobble concept
• The base at the 5 end of the anticodon is no as
  spatically confined as the other two allowing it
  to form hydrogen bonds with any of several based
  located at the 3 end of a codon, with pairing
  restrict to those on the right table

Base in Anticodon Base in Codon
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We can see the 5 end of anticodon is freer to
wobble than is the fully stackerd base at the
3end of the anticodon
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Wobble base pairing ribose-ribose distance are
close to those of AU GC base pairs
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Three Codons Direct Chain Termination

• UAA,UAG,UGA are read not by special tRNA, but
  by specific proteins known as release factors(RF1
  and RF2 in bacteria and eRF1 in eukaryotes).
• Release factors enter the A site of the ribosome
  and trigger hydrolysis of the peptidyl-tRNA
  occupying the P site, resulting in the release of
  the newlysynthesized protein.

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How the Code Was Cracked

• One of the great achievement in the molecular
  biology( turn to chapter 2 for more details)
• The use of artificial mRNAs and the availability
  of cell-free systems for carrying out protein
  synthesis
• Seeking for more details in this web site
  http//nobelprize.org/educational_games/medicine/g
  ene-code/history.html

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Stimulation of Amino Acid Incorporation by
Synthetic mRNAs

• Polynucleotide phosphorylase reaction
• XMPn XDP XMPn1 P
• 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

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Poly-U Code for Polyphenylalanine

• A Clever Experiment They carried out a series of
  experiments to see what amino acid a particular
  nucleotide template gave rise to. Strands of
  template with a known combination of nucleotides
  were run in the "cell-free" system.
• They made a very simple nucleic acid, composed of
  a chain of only one single, repeated letter the
  nucleotide uracil, or U. Using this nucleic acid,
  the system produced a protein that also contained
  a single letter, but now written in the protein
  language the amino acid F, phenylalanine. By
  showing that a strand of U triplets was indeed
  the template for the amino acid phenylalanine
  they cracked the first letter of the code.
• This was the result Nirenberg presented in
  Moscow. While he was at the conference he got a
  phone call from Matthaei (still working at the
  lab back home) who told him that CCC was probably
  the template for the amino acid proline, P.

• The experiment which used uracil (U) as a
  template produced a protein entirely made up of
  the amino acid phenylalanine (F). The first
  letter of the genetic code was hence identified.
   

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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

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Transfer RNA Binding to Defined Trinucleotide
Codons

• Specific amino-acyl-tRNA can bind to
  ribosome-mRNA complexes
• The addition of trinucleotide results in
  corresponding amino-acyl-tRNA attachment.

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The addition of trinucleotide results in
corresponding amino-acyl-tRNA attachment.

• tri- and tetra-nucleotides could be polymerized
  into polymers with repeating sequences that could
  be used in cell-free in vitro translation assays
  .
• In the case of trinucleotides, three polypeptides
  will be synthesized, each of which is a
  homopolymer of a single amino acid

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Topic 2 Three Rules Govern The Genetic Code

• 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.

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Three Kinds of Point Mutations Alter the Genetic
Code

• missense mutationan alteration that changes a
  condon specific for one amino acid to a codon
  specific for another amino acid .
• nonsense/stop mutation an alteration causing a
  change to a chain-termination codon.
• Frameshift mutation insertions or deletions of
  one or a smal number of base pairs that alter the
  reading frame.

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Three Kinds of Point Mutations
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Genetic Proof that the Code is Read in Units of
Three

• Experiment by Francis Crick, Sydney Brenner and
  coworkers involving bacteriophage T4 shows that
• the gene could tolerate three insertions but not
  one or two, the genetic code must be read in
  units of three.

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Topic 3 Suppressor Mutations can Reside in The
Same or a Different Gen

• Concepts
• Reverse 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.
• Intragenic suppression occurring within the
  same gene as the original mutation,but at a
  different site missense mutation
• Intergenic suppression occurring in another
  gene

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• Suppressor genesgenes that cause suppression of
  mutations in other genes.

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Suppressor Mutations can Reside in The Same or a
Different Gene
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Intergenic Suppression Involves Mutant tRNAs

• Suppressor genes do not act by changing the
  nucleotide sequence of a mutant gen.Instead, they
  change the way the mRNA template is read.
• nonsense mutations A mutation in the anticodon
  of tRNA that alters the anticodon so it is now
  complementary to a nonsense codon allowing the
  tRNA to insert its cognate amino acid at this
  nonsense codon during translation.

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Intergenic Suppression Involves Mutant tRNAs

• If a mutation occurs in the DNA that changes the
  AAG codon in the mRNA to UAG, the UAG codon will
  be read as a stop signal and the translation
  product will be a truncated (short) usually
  nonfunctional polypeptide.

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Nonsense Suppressors also Read Normal Termination
Signals

• The act of nonsense suppression can be viewed as
  a competition between the suppressor tRNA and the
  release factor.
• E. coli can tolerate the misreading of the UAG
  stop condon UAG but not UAA because UAG is used
  infrequently as a chain-terminating codon at the
  end of open

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Proving the Vality of the Genetic Code

• A classic and instructive experiment in 1966
  helped to validate the genetic code.

NH2Lys Ser Pro Ser Leu Asn AluCOOH 5 AAA AGU
CCA UCA CUU AAU GC3 5 AAA GUC CAU CAC UUA AUG
GC3 NH2--Lys Val His His Leu Met AlaCOOH
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Topic4 The Code is Nearly Universal

• 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.

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The Code is Nearly Universal
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The Code is Nearly Universal