Ch.12 Mutation and DNA Repair Flashcards
Xeroderma pigmentosum
autosomal recessive disorder (1 in 250,000 children). Exposure to UV radiation causes skin cancer. Caused by a loss of function mutation (UV DNA damage repair enzyme is missing)
DNA repair mechanism experience a mutation
Mutation definition
A change in the genetic material, the process by which the change occurs
Mutant
an organism that exhibits a novel phenotype
Mutation
Source of genetic variation
Provides the raw material for natural selection to act upon (no negative or benefit)
Mutation
Source of damage
That contributes to cell death, genetic diseases and cancer.
Mutations have a wild range of effects on organisms depending on?
The type of alteration, the location of the mutation on the chromosome, and the function of the affected gene product.
Types of Mutations
Changes in chromosome number and structure.
Ex: trisomy/monosomy of one chromosomes, breakage and loss of pieces, translocation, inversions.
Point mutations - changes at specific sites in a gene (caused through substitution, insertion, or deletion).
Somatic mutations
In somatic cells; the mutant phenotype will occur only in the descendants of that cell and will not be transmitted to the offspring.
In humans, many kinds of cancers are caused by somatic mutations (skin cancer - through UV damage - that cell divides and all descendants will have cancer. Won’t give cancer to kids)
Germinal mutations
In germ line cells; will be transmitted through the gametes to the offspring.
Dominant mutations: expressed immediately
Recessive mutations: expressed only when they become homozygous in a later generation.
Can occur at any stage of the reproductive cycle (sperm and egg, zygote)
Spontaneous mutations
Occur without a known cause due to inherent metabolic errors, errors during DNA replication or unknown agents in the environment..
Observed frequencies vary by gene and organisms.
Various genes in phages and bacteria 10^8 to 10^10 mutations per nucleotide pair per generation.
In eukaryotes: 10^7 to 10^10 per nucleotide pair per generation.
Mutation rate per gene varies from 10^4 to 10^7 per generation.
Induced mutations
Result from exposure to mutagens, physical and chemical agents that cause changes in DNA, such as ionizing irradiation, ultraviolet light, or certain chemicals.
Treatment with mutagens increases mutation frequencies by orders of magnitudes.
Mutation frequency per gene in bacteria and viruses can be increased to >1%.
The molecular basis of mutation
Mutations may result from:
Single base-pair changes.
Addition or deletion of base pairs (causing frame shift mutations)
Insertion of a transposable genetic element in a gene.
They may also arise when an array of repeated trinucleotides expands.
Single base-pair changes, additions and deletions
Info content can change or info is lost (bc of nonsense results).
Tautomeric shifts
Watson and Crick pointed out that the structure of the DNA bases are not static.
Hydrogen atoms can move and change positions.
Such chemical fluctuations are called tautomeric shifts.
2 diff shifts:
Keto-Enol
Amino-Imino
Tautomeric shifts can result if?
A base exits in the rare form at the moment it is being replicated or being incorporated into the growing DNA chain. Thymine: common keto. rare enol Cytosine: common amino, rare imino Adenine: common amino, rare imino Guanine common keto, rare enol
Tautomeric Shifts affect base-pairing
Hydrogen bonded A:C and G:T base pairs that form when cytosine and guanine are in their rare imino and enol tautomeric forms.
Tautomeric shifts can cause?
Base substitutions
Base substitutions
Transition
Replaces a pyrimidine with another pyrimidine or a purine for another purine.
T and C, C and T (pyrimidine)
A and G, G and A (purine)
Base substitutions
Transversion
Replaces a pyrimidine with a purine or a purine with a pyrimidine. A and T, A and T T and G, G and T G and C, C and G A and C, C and A
Depurination and deamination
Some of the most common causes for?
Mutations
Depurination
Loss of a purine base because glycosidic bond between the deoxyribose and the purine ring breaks
Deamination
(loss of amino group)
Amino group in cytosine or adenine is converted into a keto group; cytosine is converted to uracil, adenine is coverted to hypoxanthine.
Leads to base substitutions
Frameshift mutations
Insertions or deletions of one or more base pairs alter the reading frame of the gene distal to the site of the mutation.
Mutations induced by transposons
Many organisms contain DNA elements that can move from one site to another site.
Insertion of a transposon into a gene will make this gene nonfunctional.
Many classical mutants in maize, Drosophia, E.coli are caused by transposons.
Expansions of Trinucleotide Repeats
Simple tandem repeats are repeated sequences of one to six nucleotide pairs.
Trinucleotide repeats can increase in copy number and cause inherited diseases.
CAG and CTG repeats: Huntington disease (dominant) (more often repeats are found in a particular gene, severity of disease/early age onset is increased).
These diseases are characterized by anticipation, the increased severity of disease or earlier age of onset in successive generations as the trinucleotide copy number increases.
Mutagenesis
Mutations can be induced with chemicals or radiation. Mutagenesis is the practice of inducing mutations for experimental purposes (can study mutations)
Spontaneous germ-line mutation rates in humans
Until recently constricted to single genes.
With whole-genome sequencing it is now possible to examine entire genomes.
2012: sequencing of SNPs (singe nucleotide polymorphisms) shoes that newborns babies’ genomes contain an average of 60 new mutations compared to the genomes of their parents (much higher than previously thought).
Spontaneous somatic mutation rates in humans
(usually calculated per cell division)
At every cell division, a cell can acquire a mutation.
Somatic mutation rates are 4-25 times higher than germ-lines.
Somatic mutations occurring in early development are estimated to lead to as many as 6 to 20% of Mendelian disorder cases.
Was mutation spontaneous or induced?
Impossible to prove at the individual level.
With very few exceptions it is impossible to prove in an individual what caused the mutation (mesothelioma: malignant cancer, caused by inhalation of asbestos fibers)
But possible to study at the population level:
Statistical comparisons between mutation rates of populations exposed and unexposed to the mutagens (for example: mutation load in animal and human populations after nuclear diesters)
Induced mutations
Occur upon exposure to physcial or chemical mutagens.
1927: Hermann J Muller and Edgar Alternburg measured the frequency of X-linked recessive lethal mutations in Drosophila: “Artificial Transmutation of the Gene”
Muller demonstrated that exposing Drosophila sperm to X-rays increased the mutation frequency.
Mutagens
Examples
Natural or artificial agents that induce mutations. All cells are exposed to a plethora of mutagens (all the time) Cosmic rays Ultraviolet light Medical X rays Industrial pollutants Fungal toxins (Mycotoxins, black mold) Chemicals (tobacco smoke)
Electromagnetic Spectrum
Irradiation: Process with which an organism (or object is exposed to radiation.
Rays collide with atoms and cause the release of electrons, creating positively charged ions; these ions collide with other molecules and cause the release of more electrons and so on
UV rays: not enough energy for ionization.
X rays, gamma rays, cosmic rays - ionizing radiation.
Mutagenesis by Ultraviolet Irradiation
Purines and pyrimidines absorb UV at 260 nm.
Hydrolysis of cytosine may cause mispairing during replication.
Cross-linking of adjacent thymine forms thymidine dimers, which block DNA replication.
Ionizing Radiation
X rays, gamma rays, cosmic rays.
Penetrate deeply into tissues.
Causes ionization of molecules (shakes molecules lose).
Stable molecules transformed into free radicals (chemical species containing one or more unpaired electrons)
Free radicals directly/indirectly affect DNA
-Alter purines and pyrimidines
-Break phosphodiester bonds
-Produce deletions, translocations, and fragmention
Irradiation Dosage and Mutation frequency
Linear relationship: each mutation results from a single ionization event
- Every ionization has a fixed probability of inducing a mutation
- There are no safe levels of irradiation.
Types of Chemical Mutagens
Chemicals that are mutagenic to both replicating and nonreplicating DNA (alkylating agents and nitrous acid).
Chemicals that are mutageic only to replicating DNA (base analogs and acridine dyes) - (chemicals that pregnant women should avoid are mostly these. Can harm developing fetus)
Base analogs
Have structures similar to normal bases.
Can substitute for purines or pyrimidines when incorporated during DNA replication.
Increase tautomeric shifts.
Increase sensitivity to UV light.
Ex: 5-Bromouracil behaves as thymine analog (used as a mutagen in research)
Alkylating Agents
Chemicals that donate alkyl groups (CH3 or CH3CH3) to amino or keto groups in nucleotides.
Alter base-pairing properties.
Induce transitions, transversion, frameshifts, and chromosome aberrations.
Ex: Mustard gas (discovered during WWI, used in chemical warfare studies)
Intercalating Agents
Chemicals with dimensions and shapes that wedge between DNA base pairs.
Causes base-pair distortions and DNA unwinding.
Causes frameshift mutations.
Some intercalating agents are used as DNA stains and cancer drugs.
Ex: ethidium bromide, SybrSafe (DNA stain), Doxorubicin to treat Hodgkin lymphoma (stops DNA replication, stops cancer from dividing)
Adduct-forming agents
Covalently binding to DNA, altering conformation and interfering with replication and repair.
- Chromium-6: industrial pollutant, widely found in drinking water in the US.
- Acetaldehyde: Component of cigarette smoke.
- Heterocyclic amines (HCAs)
- -Cancer causing chemicals created during cooking of meats with high temperature (beef, chicken, fish)
- -17 different HCAs are linked to cancers of stomach, colon, and breast.
DNA repair systems
Counteract spontaneous and induced DNA damage.
Proofreading and mismatch repair
-DNA polymerase “proofreads” removes and replaces incorrectly inserted nucleotides
-Mismatch repair (if proofreading fails) becomes activated
-Mismatches are detected, cut, and removed (endonuclease and exonuclease) (leave gaps). Correct nucleotide inserted by DNA polymerase (gaps closed)
How are incorrect nucleotides recognized?
Strand discrimination is based on DNA methylation
Adenine methylase (enzyme in bacteria) recognizes DNA sequences and adds methyl group (CH3) tp adenine residues (tag original DNA strand).
Newly synthesized strand of replication remains unmethylated.
Mismatch repair recognizes unmethylated strand and repairs.
How are incorrect nucleotides recognized?
Postreplication repair
Responds after damaged DNA has escaped repair has failed complete replication.
RecA protein directs recombination exchange with corresponding region on undamaged parental strand (donor DNA).
Gap can be filled in by repair synthesis.
DNA repair mechanisms in E.coli
Light dependent repair (photoreactivation).
Excision repair.
Mismatch repair.
Postreplication repair.
Error-prone repair system (SOS response) - last line of defense.
Mammals seem to posses the same repair mechanisms, except photoreactivation.
Light dependent repair (photoreactivation) in E.coli
DNA photolyse: light activated enzyme.
Recognizes and binds thymine dimers. Gets activated by blue light.
Cleaves the crosslinks.
Excision Repair
1) DNA repair endonuclease containing enzyme complex recognizes, binds to, and excises the damaged base or bases.
2) DNA polymerases fills in the gaps.
3) DNA ligase seals the break
2 types:
Base excision repair pathways remove abnormal or chemically modified bases.
Nucleotide excision repair pathways remove larger defects, such as thymine dimers.
Base excision repair
DNA glycosylase recognizes abnormal bases.
Glycosylase cleaves the glycosidic bond between the abnormal base and the sugar.
AP site: apurinic or apyrimidinic site.
AP endonuclease and phosphodiesterase remove the sugar at the AP site.
The gap is filled and sealed by the DNA Pol and DNA ligase.
DNA excision repair steps
1) Deamination of cytosine
2) Binding or uracil DNA glycosylase
3) Excision of uracil
4) Sugar-phosphate removed by AP endonuclease and phosphodiesterase.
5) DNA polymerase
6) DNA ligase
The SOS response in E.coli
SOS response is a drastic step trying to survive.
If DNA is heavily damaged by mutagenic agents, the SOS response is activated.
DNA polymerase V replicates DNA in damaged regions, but sequences in damaged regions cannot be replicated accurately.
This error-prone system eliminates gaps but increases the frequency of replication errors.
E.coli can escape the lethal effects of heavy DNA damage, but the mutation rate increases.
Photoreactivation absent from mammals
Photoreactivation is activated by blue light. Blue light does not have the energy to penetrate deep into tissue through several layers of cells, and in a multicellular organism like a mammal, that would be useless. Hence, photoreactivation is a repair mechanism found in bacteria such as E.coli but is absent from mammals.
The definition of a mutation is:
a change in the genetic material
What is a point mutation?
a nucleotide change in a specific site in a gene
Result of exposure of organisms to physical and/or chemical agents that cause changes in DNA and RNA.
induced mutations
What is a base pair substitution in which A is replaced by G?
Transition
What is a base pair substitution in which A is replaced by T?
Transversion
Tautomeric shifts are:
Natural chemical shifts of hydrogen molecules around a carbon ring; they can lead to miss-base pairing
Thymine dimers form when:
2 thymines on the same strand and adjacent to each other bind together.
A post replication DNA repair pathway that provides backup to replicative proofreading
mismatch repair
Ethidium bromide is an?
intercalating agent
Mutations that occur without a known cause
spontaneous mutations
