DNA mutation and repair Flashcards
(151 cards)
1
Q
Any change made to the DNA sequence or chromosome structure
A
Mutation
2
Q
what can mutation create
A
Can lead to disease/death
create new alleles (evolution)
3
Q
are the changes of mutation permanent?
A
yes
4
Q
how are mutations classified
A
1) size
2) what causes them
3) Type of cell that contains mutated DNA
5
Q
Large segments of chromosomes are deleted, inverted, moved, or duplicated
A
Chromosomal mutations
6
Q
Smaller changes in the DNA sequences
A
Gene mutations
7
Q
Some due to natural biochemical events
A
spontaneous mutations
8
Q
Others helped along by some artificial factor (chemicals, radiation, viral)
A
induced mutations
9
Q
Arise in the DNA of somatic cells (normal diploid)
A
Somatic mutations
10
Q
what type of mutation are NEVER passed onto the next generation
A
Somatic mutations
11
Q
Mutations arise in the DNA of gamete-forming tissue (those cells that produce sperm and eggs)
A
Germ-line mutations
12
Q
what mutations can be transmitted to offspring
A
Germ-line mutations
13
Q
mutations incompatible with life
A
lethal mutations
14
Q
mutations that lead to prenatal death
A
embyronic lethal mutations
15
Q
mutations that only produce an effect under certain environmental conditions
A
(conditional mutations)
16
Q
mutations that reverse the effect of a previous
mutation
A
suppressor mutations
17
Q
2nd mutation in the same gene
Mutation 1 alters protein structure, 2 alters it back
A
Intragenic
18
Q
2nd mutation in totally different gene
Mutant protein 1 is defective, mutant protein 2 does the job of protein 1
A
Intergenic
19
Q
Types of Small gene mutations
A
1) Base-pair substitutions
2) Insertions/deletions
3) Expansion of trinucleotide repeats (TNRE)
20
Q
One nucleotide is changed to a different nucleotide
A
Base-pair substitutions
21
Q
Possible outcomes on the amino acid sequence with Base-pair substitutions
A
1) No effect
2) Change causes the wrong amino acid to be inserted
3) Change turns the codon into a stop
codon
22
Q
a mutation with No effect
usually see this if the 3rd nucleotide of a codon is changed
A
silent mutation
23
Q
Change causes the wrong amino acid
to be inserted
A
missense mutation
24
Q
Change turns the codon into a stop
codon and Causes the polypeptide to stop growing
A
nonsense mutation
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An extra nucleotide gets added or removed
Insertions/deletions
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why are Insertions/deletions very bad
it causes a frameshift
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shift in the reading frame
frameshift
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Some loci contain a series of trinucleotide repeats next to a gene or inside the gene
Expansion of trinucleotide repeats (TNRE)
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what Abnormal event can occur with the Expansion of trinucleotide repeats (TNRE)
Copy number increases
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Abnormal DNA structure causes DNA pol to what
slip and copy section 2x
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TNRE disorders usually get worse each generation
anticipation
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How does DNA damage get converted into permanent mutations?
1) A change occurs in the structure of a nt (lesion/damage)
2) DNA rep occurs – DNA pol puts "wrong" nt across from the lesion
3) 2nd DNA rep occurs – Wrong nt serves as a template for complimentary wrong nt
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Causes of spontaneous damage include
1) Errors of DNA polymerase
2) Tautomeric shifts
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Polymerases and proofreading/repair enzymes are not what
perfect
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Some major causes of spontaneous errors during replication in dna poly include
a) Strand slippage (see TNRE)
b) Defective proofreading
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Repeats cause abnormal loop ---> DNA pol copies same thing 2x
Strand slippage (see TNRE)
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a chemical reaction that occurs when the position of electrons and protons in a molecule rearrange
Tautomeric shifts
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Nitrogenous bases can exist in different chemical forms called what
structural isomers
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"Normal" forms
A-T, C-G bonding
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"Rare" isomers
Abnormal base pairing
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VERY BAD if Conversion between normal and abnormal isomers occur when
right before DNA replication
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what happens if if Conversion between normal and abnormal isomers occurs at a bad time?
DNA pol will read rare form and
insert the wrong base across
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A nitrogenous base shifts from the common tautomer to the rare version
tautomeric shift
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Tautomeric shift steps
a) A nitrogenous base shifts from the common tautomer to the rare version
b) DNA replication begins
c) DNA replication begins again
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Causes of spontaneous damage include
1) Errors of DNA poly
2) Tautomeric shifts
3) Depurination and deamination
4) Oxidative damage
5) Transposons (aka jumping genes)
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Sugar-base bond is spontaneously
broken
Depurination
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how is Sugar-base bond is spontaneously
broken
Base is lost (usually purines) and nucleotide
is left empty
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nucleotide left empty
apurinic site
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What would happen to apurinic site during
DNA replication?
can cause replication to stall or lead to mutations if bypassed, potentially resulting in single or double-stranded DNA breaks
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An amino group of C or A is
spontaneously lost
Deamination
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why is a An amino group of C or A is lost
- C or A w/o amino groups won't hydrogen
bond with normal G and T
- DNA pol sees a deaminated C (or A) and
puts in the wrong base
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Normal process of aerobic cellular respiration creates extremely reactive
atoms called free radicals which steal electrons from DNA bases
Oxidative damage
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An atom or group of
atoms that has/have an unpaired electron
Free radicals
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Free radicals will steal an electron from
Proteins, lipids, DNA
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what happens when this happens: Removal of electrons from DNA bases
alters their structure
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Thought to be major mutagen in our cells
Cancer and aging
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Mobile pieces of DNA abundantly found in all living things
Transposons (aka jumping genes)
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Cut or copy themselves and then insert
randomly in the host genome
Transposons (aka jumping genes)
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Transposons (aka jumping genes) encode what enzyme
transposase
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move discrete segments of DNA called transposons from one location in the genome (often called the donor site) to a new site without using RNA intermediates
transposase
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Insertion near genes or within genes can disrupt
host gene expression
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what is control when transposase is controled
movement
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Some external agents (chemical and physical) can induce DNA damage
1) Base analogs
2) Alkylating agents
3) Intercalating agents
4) UV light and low energy radiation
5) High-energy radiation (ionizing radiation)
6) Viruses
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Chemicals that resemble normal nucleotides and can substitute for them during DNA replication
Base analogs
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However, they exhibit abnormal base-pairing properties
Base analogs
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These chemicals add an alkyl group (CH3 or CH3CH2) to
amino or ketone groups in nucleotides
Alkylating agents
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exhibit abnormal base pairing
Alkylated nucleotides
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Alkylating agent used as a weapon in WWI
- Soldiers came down with severe burns, blindness, and tumors
Mustard gas
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what is Mustard gas an example of
Alkylating agents
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Flat, multiple-ringed molecules that tightly wedge themselves between the bases of DNA distorts its 3-D structure
Intercalating agents
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acridine orange and ethidium bromide are examples of
Intercalating agents
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They are common used to visualize
DNA during centrifugation or gel
electrophoresis
acridine orange
and ethidium bromide
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Disrupt DNA and other macromolecules
UV light and low energy radiation
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λ≈260 nm and is very mutagenic
UV light
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causes adjacent pyrimidine bases to fuse with one another
UV light
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fused pyrimidine bases
pyrimidine dimers
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Distort DNA 3-D structure
pyrimidine dimers
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prevent DNA pol from replicating normally
Pyrimidine dimers
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Cells containing too many of these
what will kill themselves via cell suicide (apoptosis)
dimers
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EM radiation with shorter wavelengths even worse
High-energy radiation (ionizing radiation)
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How High-energy radiation Mutates DNA
1) It cause electrons to be released from various
molecules in the cell producing free radicals
2) It directly breaks phosphodiester bonds in the DNA
strands (causes double- stranded breaks)
- Can produce deletions, translocations, inversions
3) Creates thymine dimers
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It cause electrons to be released from various molecules in the cell producing free radicals
ionization
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have the ability to randomly insert themselves into our genome
Viruses
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what happens when Viruses go into a promoter or coding sequence
gene expression disrupted
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produce proteins that directly inhibit DNA replication, monitoring, or repair mechanisms
viruses
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can viruses be removed
no
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Used to test if a new chemical has ability to mutate DNA (cause cancer)
Ames test
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Ames test Set-up
* Uses bacterial strain that can't make its own histidine (won't grow w/o it)
* Mix bacteria w/ either chemical or H2O and add to Petri dish lacking histidine
- No bacteria should grow
*Mutations can occur to allow the bacteria to make histidine ----> regain ability to grow
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Ames test results
- H2O control ->>>Very few colonies (spontaneous)
- Mutagenic chemical -->> lots of colonies (BAD!!)
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Most types of DNA damage can be fixed by
the cell
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when Must DNA damage be fixed
PRIOR TO DNA REPLICATION
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what dna damage can't be fixed
Transposons and retroviruses
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Different types of DNA damage
- Altered individual bases
- Altered 3-D DNA structure
- Double-strand DNA breaks
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Reverses the alteration w/o cutting out or replacing any nt
Direct DNA repair
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what is Direct DNA repair used to repair
thymine dimers and alkylated bases
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Both bacteria and eukaryotic cells use
light-dependent pathways
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how are thymine dimers repaired
Direct repair
Eukaryotic cells – use an enzyme called photolyase to cut abnormal covalent bonds between the two thymines
- Bacteria – use an enzyme called photoreactivation enzyme (PRE) to do same
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Eukaryotic cells – use an enzyme called what to cut abnormal covalent bonds between the two thymines
photolyase
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bacteria cells – use an enzyme called what to cut abnormal covalent bonds between the two thymines
photoreactivation enzyme (PRE)
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how are alkylated bases repaired
Direct repair: Methylguanine DNA methyltransferase enzymes directly cuts off extra CH3
from guanine
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Removal of altered base/nucleotide and replacement with
good DNA
Excision repair
102
steps of Excision repair
1. Recognition of the lesion by 1 or more proteins and the subsequent excision of that error by a nuclease enzyme
2. A DNA polymerase fills in the space with proper nucleotides
- What enzyme would you predict does this in prokaryotic cells?
3. DNA ligase seals the final nick
103
2 types of excision repair systems
- Base excision repair
- Nucleotide excision repair
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used for correction of minor alterations to individual bases (free radical, alklyated, base analog)
Base excision repair
105
steps of Base excision repair
1) DNA glycosylase enzymes recognize altered bases
2) Glycosylase then cuts out the base only (breaking the
sugar/base bond)
3) AP endonuclease enzyme recognizes the nucleotide
missing the base and makes a cut in the sugar/ phosphate backbone at that site
4) DNA pol I/ligase finish the job (and repair the damage)
106
fixes larger lesions that
distort the actual DNA structure and block replication
Nucleotide excision repair (NER)
107
steps of Nucleotide excision repair (NER)
1. DNA is damaged and a lesion forms
2. Proteins called Uvr (UvrA, B, C, D)
recognize the lesion and cut it out
- A-B complex recognizes the lesion
- A comes off and is replaced with C
- B-C together cut the DNA on either side of the lesion
- D is a helicase that liberates the cut piece
3. DNA pol I fills in the gap/ ligase seals
108
what forms when dna is damaged
legion
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recognize the lesion and cut it out
Proteins called Uvr (UvrA, B, C, D)
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recognizes the lesion
A-B complex
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comes off and is replaced with C
A complex
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together cut the DNA on either side of the lesion
- Cut out extra "good" DNA on both sides
B-C
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is a helicase that liberates the cut piece
D complex
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human disorders exist in which the NER system is defective
xeroderma pigmentosum
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Contain one of several rare mutations in some part of the NER pathway
Xeroderma pigmentosum (XP)
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They have severe skin abnormalities when exposed to the sun
- UV light exposure Induces freckling, ulceration, and skin cancer
Xeroderma pigmentosum (XP)
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fixes mismatches (DNA may
look okay otherwise)
Mismatch repair
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"Wrong" nucleotide is always on
the new strand
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Newly-made DNA strands stay
unmethylated
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is always on the new, unmethylated strand
Wrong nucleotide
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Mismatch repair mechanism
1) MutS protein locates mismatches
2) MutL binds to MutH
3) MutH makes a cut in the unmethylated strand
4) MutU acts as a helicase to release the unmethylated strand before an exonuclease destroys it
5) DNA pol III fills in with proper sequence, ligase seals
122
locates mismatches and Forms complex with MutL afterward (linker)
MutS protein
123
binds to MutH
MutL
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bound to a nearby hemi-methylated site
MutH
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DNA must loop out to allow
L-H interaction
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makes a cut in the unmethylated strand
MutH
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acts as a helicase to release the
unmethylated strand before an exonuclease
destroys it
MutU
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fills in with proper sequence
DNA pol III
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seals
ligase
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Two repair pathways fix double-stranded breaks
1) Homologous recombination repair
2) Non-homologous end-joining
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steps of Homologous recombination repair
a) Homologous chromosome first brought in
b) RecBCD recognizes double stranded breaks
c) RecA binds to single-stranded end and promotes invasion of the homologous chr.
d) RuvABC, DNA polymerase, and ligase help to recreate the gaps and resolve the structure
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what is first brought in
Homologous chromosome ( Usually the sister chromatid)
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recognizes double stranded breaks, Partially degrades 1 strand on each side, and Creates single-stranded overhangs
RecBCD
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binds to single-stranded end and
promotes invasion of the homologous chr.
RecA
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The good strand loops up
D-loop
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help to recreate the gaps and resolve the structure
RuvABC, DNA polymerase, and ligase
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The once damaged chromosome will contain a piece of the
homologous chr.
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The two broken ends are simply glued back together
Non-homologous end-joining
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does Non-homologous end-joining need sister chromatid
no
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bind to each side of the break (to stabilize)
End-binding proteins
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recruited to prevent drifting of the two pieces
Cross-bridging proteins
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what happens to the ends during Non-homologous end-joining
processed, filled, and ligated
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advantage of Non-homologous end-joining
Can happen any time in cell
cycle (no sister chr. required)
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disadvantage of Non-homologous end-joining
Can lead to small deletions
near the break site (result of processing)
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Some lesions (e.g. TT) block
normal DNA replication (via DNA pol III)
146
If other repair fails, what will initiate to allow DNA replication to
finish
translesion synthesis
147
- Stalling of normal DNA polymerase by lesion triggers
recruitment of "emergency" polymerases
- Have different binding pocket more tolerant of
altered DNA structure
- Emergency pols (e.g. DNA pol II, IV, V) replicate
over the lesion
- Problem: They are very error prone
- DNA gets replicate, but with mistakes
- Original lesion remains (not fixed)
- Translesion synthesis enables rep to
continue
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triggers recruitment of "emergency" polymerases
Stalling of normal DNA polymerase
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replicate over the lesion
Emergency pols (e.g. DNA pol II, IV, V)
150
problem of Translesion synthesis (called SOS repair)
They are very error prone
- DNA gets replicate, but with mistakes
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