3/6/16
BIOLOGY 207 - Dr. Locke
Lecture#9 – Mutations originate as damage to DNA
Required readings and problems:
Reading: Open Genetics, Chapter 4
Problems: Chapter 4
Optional
Griffiths (2008) 9th Ed. Readings: pp 513-541; 54-56
Problems: 9th Ed. Ch. 15 : 1,2,8,9,12,16,19,26
Campbell (2008) 8th Ed. Readings: Concept 17.5
Concepts:
What are mutations??
1. Mutations are changes in the DNA sequence.
2. Mutations
can arise without external influence (spontaneous) or
can be caused by mutagenic agents (induced).
3. Properties of mutagens and repair systems influence the mutations induced.
4. Damaged DNA is normally repaired
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Lecture#9
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Mutation
Process: the change in structure of a gene from
one form (commonly the normal or wild type)
to a variant form (mutation).
Mutant
- a cell or organism bearing a mutant gene that expresses itself in the phenotype
Overview
There are many ways (mechanisms) by which genetic change can occur.
1) Gene mutation - this lecture & next
2) Chromosomal Rearrangements
- changes in structure
- changes in number
3) Recombination - to come
4) Transposable Genetic Elements - Mobile elements
- very interesting
Mutations can be described at different levels
- DNA, chemical level  sequence change
- gene product  level/function
- phenotypic level  how the mutant appears
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Lecture#9
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Mutations - chemical changes to DNA
- change in quality, quantity, or order of DNA
1) Substitutions - (G) (A) (T) (C)
Fig
(A) Protein coding sequence
1) no amino acid change - silent substitutions
2) change an amino acid - may abolish, reduce, increase or change its activity
3) stop codon - abolishes the function of the truncated product
(B) Transcribed but not translated (Non-protein coding genes)
1) Alter RNA sequence - affect function of RNA molecules (e.g. rRNA, tRNA)
(C) Non-transcribed sequences
1) change sequences that regulate gene expression
- such as the promoter sequence
2) change DNA sequence in region that has no phenotypic effect - DNA between
genes
2) Addition or Deletion of bases
- changes (+1, +2, -1, -2) the amino acid reading frame (triplet codon)
(A) altered protein
(B) shortened protein if codon is stop - truncated polypeptide
3) Rearrangements
- which are: Translocations, Inversions, mobile elements
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Gene Mutation
1) Spontaneous Mutations - arise without external influence - naturally occurring
2) Induced Mutations - derived by exposure to mutagenic agents or procedures
- occur at a much higher frequency than spontaneous
Spontaneous Mutations
1) Errors during DNA Replication
The mismatches that do occur are normally either
1) Edited by DNA pol III
2) Repaired by other DNA repair systems
- error in base pairing - forms during DNA synthesis
- if not repaired (by exonuclease of polymerase or repair systems, lead to a base
substitution
Transitions - purine=>purine; pyrimidine=>pyrimidine
Transversions - purine=>pyrimidine; pyrimidine=>purine
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2) Frame shifts during replication
Frame shifts can be either additions or deletions (indel). Both are thought to:
- occur during DNA replication
- occur at repeated sequences
Fig
Typically detected in protein coding stretches of DNA because they alter the reading
frame of triplet codons.
Model to account for frame shifts based on work of Streisinger in 1960's on the
lysozyme gene of bacteriophage T4 (before DNA sequencing technology)
Frame shift mutations account for mutation hot spots in some genes. Hot spots are
sites in a gene that are much more mutable than other sites.
Example
lac I gene studied by Miller - distribution of 140 spontaneous mutations Fig
Note:
a) cluster - at site of 3 tandem CTGG repeats in coding region
- some mutants are due to addition of one repeats
- other mutants are due to deletion of one repeat
b) mutant that gains additional repeat
- has a high rate of reversion to wild type
- due to loss of extra repeat
In humans: CGG triplet repeat
-> fragile -X syndrome Fig
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3) Spontaneous Lesions
- due to naturally occurring damage to the DNA
- not during DNA replication
1) Depurination
- break in the glycosidic bond between the base and the deoxyribose sugar - results in
the loss of an A or G base from the DNA -> called apurinic site - no base
-> at replication, a template that is apurinic can not specify a base
-> replication error -> mutation
2) Deamination
- removal of an amine -NH2 group - cytosine -> deamination -> uracil - uracil will pair
with A at replication
- result: C -> U acts like T-> transition GC -> AT
Note - in these cases the miss-match will result in substitutions
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Lecture#9
Fall'11
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Induced Mutations
-various chemicals or treatments induce mutations
1- Incorporation of base analogs Fig - chemicals that are similar to normal bases
get incorporated into DNA like normal bases during replication, but don't have
pairing properties of normal bases, thus incorrect pairing at replication ->
substitution
2- Intercalating agents Fig - planar molecules that intercalate (slip in) themselves
between stacked bases in the double helix and cause single base pair insertions
or deletions by possibly destabilizing Streisinger model and result in frame shifts > base pair addition/loss
3- Base damage – UV, radiation, Aflotoxin
UV light Fig - favor GC -> AT - produces a photo dimer in adjacent thymine residues abnormal base pairing
Aflotoxin Fig - favors GC -> TA - generates apurinic sites by addition to N7 position
of guanine (purine).
Mutational specificity Fig
- mutagen produces a characteristic type of mutation
Note - Properties of the mutagen influence the type of mutation induced
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DNA Repair mechanisms
- deal with changes/damage to the DNA
(potential mutations)
- enzyme systems that repair DNA damage
- divided into several pathways/mechanisms
1) Remove damaging compounds
eg. - superoxide dismutase enzyme + catalase enzyme
- converts superoxide radical (O2-) -> hydrogen peroxide -> water
2) Excision repair pathways
Fig
General
- excise altered (and several adjacent) bases
- gap repaired by DNA synthesis (pol I)
- sealed by DNA ligase
3) Post replication repair - mismatch repair
- system capable of recognizing errors after DNA replication (Post replication Repair)
Fig
Needs to do:
1) recognize mismatched base
2) determine which is the correct base in the mismatch
3) Correct the error
There are many repair systems
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Failure of DNA Repair systems
Overwhelm the system with excess DNA damage.
Yeast & UV-C light (Biol207 Lab Project #5)
Optional reading: www.phys.ksu.edu/gene/d4.html
Mutations in DNA repair genes
Mutator Loci
E. coli
- repair systems very efficient - base substitution rate is
10-10 -> 10-9 per base pair per cell per generation
Mutator strains
- phenotype due to defective DNA repair systems
- mutations in genes encoding enzymes of DNA repair
- Mutator loci “mut” genes
Mutations in DNA - repair result in disease in humans
e.g. xeroderma pigmentosum Fig
Different Groups (genes) indicate that there are several genes that give the UV
hypersensitive phenotype when mutant.
Take home messages:
1- Many ways to damage DNA
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2- Many ways to repair damaged DNA
3- If not repaired, DNA -> get mutation
4- Specific mutagen -> specific types of DNA change
5- If one inactivates a repair system
-> get higher mutation rate
-> specific types of change, too.
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