Chapter 19: DNA Mutation & Repair (Exam 3) Flashcards
Depurination
cause of spontaneous mutation, removal of purine base from G or A
Deanimation
cause of spontaneous mutation, removal of amino group from cytosine base, DNA repair enzymes can recognize U as inappropriate and remove it, if repair system fails, C-G to A-T mutation will result in subsequent replication
Deamination of 5-methyl cytosine
cause of spontaneous mutation, thymine is normal constituent of DNA –> poses problem for repair enzymes, cannot determine which of two bases is incorrect –> hotspot for mutation
tautomeric shift
cause of spontaneous mutation, temporary change in base structure, rare, promote AC and GT bp, must occur immediately prior to DNA replication for mutation to occur
Mutagens
involved in development of human cancers, cause gene mutations that can impact future generations
Classifications of mutagens
chemical or physical
Chemical mutagens
alter DNA structure directly, base modifiers, intercalating agents
Base modifiers
covalently modify structure of a nucleotide
Example of base modifer
Nitrous Acid, replaces amino groups with keto groups
Intercalating Agents
contain flat planar structures that intercalate themselves into a double helix –> distorts helical structure –> daughter strands may have single nucleotide additions or deletions
Example of intercalating agent
Base analog
engineered to look like DNA bases but not nearly as stable, become incorporated into daughter strands during DNA replication
Example of base analogs
5-bromouracil, thymine analog, incorperated into DNA, causes incorrect base pairing, AT to GC
Classifications of physical mutations
ionizing radiation and non-ionizing radiation
two categories of physical mutagens
ionizing radiation and nonionizing radiation
examples of ionizing radiation
x-rays, gamma rays
properties of ionizing radiation
short wavelength, high energy, penetrates deeply into biological tissues (can reach gametes)
creates chemically reactive molecules: free radicals
what can free radicals cause
base deletions
single nicks in DNA strand
cross-linking
chromosomal breaks
examples of nonionizing radiation
UV light
properties of nonionizing radiation
less energy, cannot penetrate deeply
causes formation of cross-linked thymine dimers
thymine dimers
cause mutations when DNA strand is replicated
only occur at T-T sites
polymerase cannot read the TT, has to guess
DNA repair
cells contain several DNA repair systems
usually a multistep process
Steps of DNA repair
- irregularity in DNA detected
- abnormal DNA removed
- normal DNA synthesized (using DNA polymerase)
- DNA ligase seals new DNA to original strand
Types of DNA repair
direct repair
base excision repair (BER)
nucleotide excision repair (NER)
mismatch repair
homologous recombination repair
nonhomologous end joining
direct repair
not multistep
damaged bases can be directly repairs
covalent modifications of nucleotides can be reversed by specific enzymes
two enzymes that can direct repair
photlyase and alkyltransferace
photylase
repairs thymine dimers
alkyltransferace
removal of methyl group
base excision repair (BER)
uses enzymes known as DNA N-glycosylases:
can recognize abnormal base and cleaves bond between it and the sugar in DNA
A pendalases- nick backbone
what can BER repair
thymine dimers, uracil
steps of BER
- DNA N glycosylase cleaves base
- a penadalase nicks backbone
- DNA polymerase removes base
DNA excision repair (NER)
repairs many types of DNA damge: thymine dimers, missing bases, chemically modified bases, some crosslinks
found in all eukaryotes and prokaryotes
NER four key proteins (in E. coli)
UvrA, UvrB, UvrC, UvrD
involved in UltraViolet light Repair
recognize and remove short segment of DNA
DNA polymerase and ligase complete repair
diseases caused by defects in NER
xeroderma pigmentosum (XP)
cockayne syndrome (CS)
increased sensitivity to sunlight
leads to incurable skin cancer
mismatch repair systems
detect and correct a base pair mismatch
found in all organisms
specific to newly synthesized strand
base mismatch
structure of DNA double helix obeys AT/GC base pairing
during replication, an incorrect base can be added
DNA polymerase have 3’ - 5’ proofreading ability which usually corrects mismatched bases
proteins in mismatch repair (in E. coli)
MutL, MutH, MutS
detect mismatch and remove it from strand
can distinguish between parental and daughter strands:
prior to replication, both strands methylated
immediately after replication, parental methylated but daughter is not
cut the non-methylated (newly synthesized) strand
double-strand breaks
very dangerous, breakage of chromosome into pieces
caused by ionizing radiation and chemical mutagens
occur 10-100x every day in every cell in humans
cause chromosomal rearrangements and deficiencies
repair systems for double-strand breaks
homologous recombination repair (HRR)
nonhomologous end joining (NHEJ)
homologous recombination repair (HRR)
results in some recombined DNA
precise repair
Steps:
1. double strand breaks
2. processes/removes 3’ ends
3. sister chromatid acts as template using strand exchange
4. DNA polymerase synthesizes DNA
nonhomologous end joining (NHEJ)
not precise, lose some DNA
does not require sister chromatid nearby
1. double strand breaks
2. protein binds ends
3. proteins fill gap and synthesize new strand
repair of activley transcribed genes
repaired more efficiently than non transcribed genes, easier to access
transcription makes DNA more susceptible to damage
more likely to be important for survival of organism
mutations
heritable change in genetic material
provide allelic variations
foundation for evolutionary change
cause of diseases
types of mutations
chromosome, genome, single gene
point mutation
change in single base pair
transition: change of a pyrimidine (C. T) to another pyrimidine or a purine (A, G) to another purine
transversion: change of pyrimidine to purine / vise versa
silent mutation
base substitution that does not change amino acid sequence
missense mutation
base substitution that does change amino acid sequence
nonsense muation
change normal codon to a stop codon
frameshift mutation
addition or deletion of nucleotides in multiples of 1 or 2, change reading frame
up promoter mutations
make promoter more like consenus sequence, increase rate of transcription
down promoter mutation
make promoter less like consensus sequence, decrease rate of transcription
chromosomal rearrangement
may break the gene itself or alter expression because of new location (position effect)
reasons for position effects
movement next to regulatory sequence, movement into heterochromatic region
germ line mutations
occur directly in sperm or egg cell (or a precursor)
passed through generations
somatic mutations
occur in a body cell
individual with somatic mutation referred to as genetic mosaic
not passed on
mutation rate
likelihood that a gene will be altered by a new mutation
expressed as number of new mutations in a given generation
range of 10^-5 - 10^-9 per generation
things that effect mutation rates
larger genes have greater chance
locations that are more susceptible (hot spots)
spontaneous mutation
result from abnormalities in cellular/biological processes
induced mutations
caused by environmental agents
mutagen
agents known to alter DNA structure
