XIV' Gene Mutation and Repair Chapter 17

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XIV. Gene Mutation and Repair (Chapter
17)   Mutation chromosomal aberations sequence
chance in a single gene. In a sense,
mutation is a failure to store genetic
information faithfully.
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Classification of mutations based on how they
occur   1.    Substitution   The original
bases on a sequence are changed into different
ones.   If limited to one base pair point
mutation (most often seen)
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  Three consequences of point mutation  
a.     Silent mutation - Mutation without
phenotype change. b.     Neutral
mutation   The substitution does not change the
function of the protein product, because of
the chemical similarity between the two amino
acids.
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c.     Missense mutation        The codon is
changed for a different a.a. The result
may or may not be deleterious. d.     Nonsense
mutation A sense codon is changed into a stop
codon, which causes the premature termination
of translation. Damage depends on the
location of the mutation.  
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2.    Insertion and deletion   (frame-shift
mutation)
The downstream codon sequence is totally
changed. The normal stop codon will be
ignored. Stop codon may show up too early or
too late.
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  Both substitution mutation an
insertion/ deletion mutation can be spontaneous
and induced.    
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Induced mutation For exp. UV radiation
  Typical UV induced mutation is thymine
dimerization.
Fig. 17.13
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The existence of thymine dimmer disrupts the
normal structure of DNA strand. It bulges out
from the double strands, and prevents base
pairing during the synthesis of the new strand
of DNA.
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Fig. 17.14
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DNA polymerase stops before the dimmer and
starts after, leaving a gap in the newly
synthesized complementary strand. The gap is
then repaired by randomly replacing nucleotides
opposite to the dimmer. The random repair or
no repair can be the source of mutation.
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• Chemicals can induce mutations
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• Nitrous acid (HNO2) is a common chemical
• that modifies nucleotides. (p524)
• It causes deamination of adenine, guanine
• and cytosine that have amino groups in their
• structure.
• Removing of amino group can change their
• charge and base pairing properties.

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 Sodium nitrite that is used in food
preservatives is the salt of nitrous acid,
considered as a potential carcinogen.
b. Base analogs For Exp., 5-Bromouracil
(5-BU), an analog of thymine can be in the
position where a T is normally taken. 5-BU
pairs with C instead of A, a TA base pair is
eventually replaced by a GC pair (Fig. 17.15).
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c. Intercalating agent Ethidium bromide a
laboratory chemical used to stain DNA. It can
stick in between base pairs and cause DNA
damage. Ethidium bromide is considered as
carcinogen.
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Mutation can be created in test tubes -site
directed mutagenesis. Mutations provide the
bases for genetic studies Structure and
function relationship of genes orproteins.
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• A segment of DNA with changed nucleotide
• sequence can be synthesized by a machine
• A fragment is excised out from the wild
• type gene by using restriction endonuclease.
• (restriction enzyme)
• The synthesized fragment is inserted into
• the gap.
• DNA ligase is used to link up the ends

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 DNA Repair   Series of repair systems have been
developed in all organisms.   The most common
scheme is the 3'- 5' exonuclease activity in
combination with DNA proofreading ability of DNA
polymerase.
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Other DNA repair mechanisms  1.   
Photoreactivation - Direct repair of
thymine dimmer   This is a simple reversal of
pyrimidine dimers.
Photolysase, an enzyme that can bind to the
dimmer and separate the dimmer into single
pyrimidines. Since the expression of this
enzyme is induced by visible light, the process
is called photoreactivation.
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2.    Excision repair - The complementary
strand is used as template in repair   This
system is based on the fact that both strands in
DNA has the ability to store the genetic
information.
Distortion in DNA helix due to serious damage is
sensed. A 12-bp fragment is cut out and the
gap filled by DNA Polymerase and sealed by DNA
ligase.
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In E.coli, the enzyme that does the incision is
UvrABC, an endonuclease with three subunits A,
B, and C.
UvrABC detects the damage, remove and
replaces short patches of DNA (12-bp). Loss of
UvrABC repair pathway in E.coli can greatly
increase the mutation rate.  
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In humans, Xeroderma pimentosum, a
genetic disease, is an autosomal recessive
disorder and is due to the loss of the
excision-repair pathway. The patient has dry
skin and is sensitive to sunlight and is very
susceptible to malignant tumors.
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3.    Mismatch correction enzymes   In E. coli,
after DNA replication, there is a final mismatch
check up, which is done by a group of enzymes
coded by the genes mutHLSU (eukaryotes also have
a similar system). The mismatch repair enzymes
can distinguish the old and new DNA strand.
Only the mismatches in the new strand
(unmethylated) will be repaired.
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Once the mismatch is detected, an excision
process will be initiated by mutH. MutS, L, U
will also be needed to complete the process. The
gap will be filled by DNA polymerase I and
sealed by DNA ligase.
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In humans, high spontaneous mutation rate is
found in the patients with nonpolyposis colon
cancer. About half patients were found to have
defective gene similar to the mutS gene in E.
coli.
The other half patients were found to have
defect gene similar to mutL.
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4. Repair by Recombination   Gene mutation such
as thymine dimmers can happen to both strands of
DNA in same area.
In some other cases, X-ray induced mutation can
break both DNA strands and leave blunt ends.
These severe DNA damages have to be repaired
in the absence of complementary strand.,
which Can be done by recombination of different
pieces of homologous chromosomes
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For recombination to occur, the damages on two
different DNA strands have to be in different
locations. By a single crossing over, the
recombination can create one good DNA molecule
(chromosome) and one unrepairable DNA molecule.
In E.coli, the enzyme involved in recombination
repair is recA.    
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Fig.17.28