DNA Repair and How do Mutations Occur? Flashcards
types of genetic diseases (4)
chromosome disorders
single gene disorders
multifactorial or complex
sex linked and mitochondrial
Chromosome Disorders
4
Rearrangements/Translocations, Deletions, Insertions, Duplications
Single Gene Disorders
3
Dominant, Recessive, Codominant
Multifactorial or Complex
2
Multiple genes, gene-environment
general categories of mutations (2)
somatic
germline
Somatic mutation
non-inheritable
somatic mutation example
cigarette smoking and lung cancer, p53 mutations
germline mutation
inherited
— entries in OMIM currently
12,000+
causes of mutations (2)
spontaneous
induced
Spontaneous Mutations
arise naturally during DNA replication (mitosis) or during meiosis
Induced Mutations (2)
every day exposure
radiation
chemicals
silent mutation
no change
missense mutation
single amino acid change
nonsense mutation
stop codon produced truncated protein
transition
Pur/Pur or Pyr/Pyr
transversion
Purine / Pyrimidine
deletion or insertion
Extra or Missing amino acids
frameshift mutation
Altered protein
other types of mutations (4)
- Promoter/Enhancer - Nuclear Receptors
- Splice Site
- Expanded Repeat
- Transposons
nomenclature of mutations
• Amino acid designations
• genomic (gDNA) vs. mRNA (cDNA) vs. protein
• coordinates
• substitution(s)
• example:
• A1215T alanine at postion 1215 in the protein is
changed to a threonine
Alleles are
sequence variants of a gene
You inherit one
allele of each autosomal gene from
your mother and one
from your father
Single nucleotide polymorphisms (SNPs) are
single base
differences at a specific position in the genome
SNPs
occurring within a gene (can) give rise to an
allele
There are
— of SNPs in the genome
hundreds of thousands (millions)
Maintaining the genetic stability that an organism needs for its survival requires (2)
an extremely accurate mechanism for replicating DNA
mechanisms for repairing the many accidental lesions that occur continually in DNA
Most such spontaneous changes in DNA are — because they are immediately
corrected by a set of process that are collectively called — —
temporary
DNA repair
Of the thousands of random changes created every day in the DNA of a human cell by
(4), only a few accumulate as mutations in the DNA sequence
heat, metabolic accidents, radiation of various sorts, and exposure to substances in the environment
For example, we now know that fewer than one in 1000 accidental base changes in DNA
results in a — —
permanent mutation
the rest are eliminated with remarkable efficiency by
DNA repair
The importance of DNA repair is evident from the large investment that cells make in
DNA enzymes
For example, analysis of the genomes of the bacteria and yeasts has
revealed that several percent of the coding capacity of these organisms is devoted solely
to
DNA repair functions
he importance of DNA repair is also demonstrated by the increased rate of mutation
that follows the
inactivation of a DNA repair gene
Many DNA repair
proteins and the genes that encode them
Many DNA repair proteins and the genes that encode them- which we now know operate
in a wide range of organisms, including humans- were originally identified in bacteria by
the isolation and characterization of mutants that displayed an increased mutation rate
or an increased sensitivity to
DNA-damage agents
DNA is a highly stable material (compared to RNA), but it is a complex organic molecule
that is susceptible to
spontaneous changes that would lead to mutations if left
unrepaired even under normal cell conditions
DNA of each human cell loses about — purine bases (adenine/guanine) everyday
due to their deoxyribose hydrolyzation of N-glycosyl linkages, a spontaneous reaction
called —
5000
depurination
A spontaneous deamination of cytosine to uracil in DNA occurs at a rate of about —
bases per cell per day
100
DNA bases are also occasionally damaged by
3
• an encounter with reactive metabolites produced in the cell (including reactive forms of
oxygen, H2O2, -OH, and -O2)
• exposure to chemicals in the environment.
• ultraviolet radiation from sun can produce a covalent linkage between two adjacent
pyrimidine bases in DNA to form thymine dimers (presented later in this lecture)
Oxidative damage by
reactive oxygen species
Uncontrolled methylation (CH3-) by
the methyl group donor S-adenosyl-methionine
Hydrolytic attack
deamination and depurination
most frequent spontaneous chemical reactions
hydrolytic attack
Without DNA repair, spontaneous DNA damage would rapidly
change
DNA sequences
About 3% of the C nucleotides in vertebrate DNAs
are methylated to help in
controlling gene
expression
When these 5-methyl C nucleotides are
accidentally deaminated, they form the natural
nucleotide
T
However, this T will be paired with G on the
opposite strand, forming a
mismatched base pair
About one-third of inherited human disorders are
single base mutations
The spontaneous deamination products of A and G
are recognized as — when they occur in DNA
and thus are readily (2)
unnatural
recognized and repaired
base excision repair
unnatural bases are recognized and removed by a specific DNA glycosylase
(2) are the two most frequent
spontaneous chemical reactions known to create serious DNA damage in cells
Deamination and depurination, hydrolytic reactions
Deamination
cytosine to uracil in DNA is estimated to occur at a rate of 100
bases per genome per day
Depurination
lose 5000 purine bases (A or G) per day in each cell due to thermal
disruption of their N-glycosyl linkages to deoxyribose
Pyrimidine (C or T) dimer formation
covalent linkage of two adjacent pyrimidines by UV light from the sun
These premutagenic lesions alter the structure
of DNA and consequently (2)
inhibit polymerases
and arrest replication
Dimers may be repaired by (2), but unrepaired
dimers are mutagenic
photoreactivation
or nucleotide excision repair
AP site (apurinic/apyrimidinic site)
a location in DNA that has neither a purine nor a pyrimidine base
what does a bread in DS DNA cause
delays progression of G1 to S phase and from S to M phase (through G2) in the Cell Cycle
little of the mammalian genome codes for
proteins (1.5% of exons) and has function (3.5% of highly
conserved sequences such as 5’ and 3’ UTR, functional RNAs and conserved protein binding site of the
DNA ) that this mechanism is apparently an acceptable solution to the problem of rejoining broken
chromosomes (deletion)
If each member of a chromosome pair carries the
same allele, then the individual is called
— for that gene
homozygous
If each member of a chromosome pair carries a
different allele, then the individual is called
— for that gene
heterozygous
The phenotype of a — gene will be
observed in the homozygous or heterozygous state
dominant
The phenotype of a — gene will be observed
only in the homozygous state
recessive
mendels laws (2)
principle of segregation
principle of independent assortment
Principle of Segregation
Sexually reproducing organisms possess genes that
occur in pairs and that only one member of this pair is
transmitted to the offspring
Principle of Independent Assortment
Genes at differ loci are transmitted independently
homologous recombination
Genetic exchange between a pair of homologous
DNA sequences
DNA breaks often occur from (2)
radiation damage or
reactive chemicals
DNA breaks also arise from DNA replication forks that become (2)
stalled or broken
Homologous recombination is a mechanism to (3)
- Accurately repair double strand DNA breaks
- Exchange bits of genetic information
- Assures accurate chromosome segregation during meiosis
Homologous recombination has common features in
all
cells
what guides homologous recombination?
DNA base pairing
In the test tube base pairing of single stranded DNA
drives
DNA renaturation or hybridization
DNA renaturation or hybridization is a
(2) driven process
temperature and salt
High temperature
drives
double stranded DNA into single stranded DNA
In cells that cannot survive at high temperatures, — are used that bind tightly
to the DNA and hold it an open configuration to serve as a
template for DNA synthesis
single
stranded DNA binding proteins
Double-strand DNA breaks can be repaired by (3)
• Non-homologous end joining without a template which
creates a mutation at the site where the DNA duplexes
are joined.
• Inadvertent joining of two segments from different
chromosomes that results in chromosomal
translocations, which often give rise to disease
• Homologous recombination repairs DNA double strand
breaks accurately without loss or alteration of the DNA
sequence
Cells carefully regulate the use of homologous
recombination in
DNA repair
Repair involves a number of
proteins
The enzymes catalyzing repair are present at —
concentrations in the —
high
nucleus
A number of accessory proteins are involved in
control of repair
Loss of essential proteins needed for repair are generally
— events
lethal
Loss or alterations (mutations) of accessary proteins
often leads to
cancer
steps of homologous recombination (2)
1) Repair double-stranded breaks accurately
2) Generate crossover in meiosis
— — are often formed during homologous recombination
Holliday junctions
Holliday junction
(cross-strand exchange)
two DNA strands switch partners between
two double helices
DNA is under constant pressure to
acquire changes in its
DNA sequence
Most changes are repaired before they
become a
stable part of the DNA that is subsequently
passed on to daughter cells
Various types of mutations occur in DNA, some of which
will give rise to
altered protein variants of any given
gene
When mutations occur in somatic tissues, they cannot
be —, but can give rise to diseases such as —
inherited
cancer
When mutations arise in the DNA of the gametes, they
will be
passed on to the offspring
