Mutation Flashcards
Somatic mutations
Occur in somatic cells and are not passed to progeny
Germinal mutations
Occur in gametes, are passed to progeny
Phage mutants
Useful in genetic studies.
Base substitution (transition)
Pyrimidine swapped for a pyrimidine or purine for purine
Base substitution (transversion)
Pyrimidine swapped with purine (vice versa)
Frameshift
Insertion or deletion of one or two bp that alters the reading frame of the gene downstream.
Tautomeric shift
Movement of H atoms from one position in a purine of pyrimidine base to another.
E.G causes rare A:C (rare imino form) and G:T (rare enol form).
Expanding nucleotide repeats
expansion of triplet repeats (i.e. CAG and others) is cause of numerous human diseases (e.g. huntington’s)
Mechanism of expansion involves DNA replication
In a region of many triplet repeats, polymerase may have some difficulty knowing where it is in the order of repeats so it pauses and slips backwards, forming a hairpin loop
Hairpin obviously elongates the DNA by a bit and then when that DNA has to be replicated, there’s more triplet repeats than before which exacerbates the issue, causes continual addition of unnecessary repeats
A “dynamic” mutation because repeat copy number is in flux with each round of replication
Forward mutation
Genetic alteration that changes the wild-type into a mutant
Reverse mutation
Mutated site back to wild-type
Missense mutation
Base substitution that results in an AA change
Nonsense mutation
Base substitution that results in a regular codon becoming a stop coding
Silent mutation
Base substitution at the 3rd codon position that changes to codon to one still specifying the same AA
Loss of function mutation
Causes complete or partial loss of normal protein function
Gain of function mutation
Cell produces protein/gene product whose function is not normally present
Suppressor mutation
Second site mutation that hides/suppresses the effect of the first mutation.
Spontaneous DNA damage results from
DNA Replication errors - tautomeric shifts, wobble mispairing or strand slippage during replication
DNA replication pauses- Replication stalls at nick in DNA, unusual DNA structure or bulky lesion can generate broken DNA
Endogenous chemical reactions -
Depurination - spontaneous loss of purine base from a nt through hydrolysis of glycosidic bond ( ~10000 x/cell/day). Loss of pyrimidine is possible but less frequent. Leaves abasic site which is susceptible to replacement with A or C, creates transition or transversion
Deamination - spontaneous loss of –NH2 group on base, causes transition mutation. Deamination of 5MeC converts C to T, pairs to A
Oxidation - endogenous reactive oxygen species (ROS) damage DNA, can produce oxidized bases such as 8-oxoG which frequently mispairs with C or A, causes transversion mutations (G:C → T:A)
Alkylation - endogenous alkylating agents (i.e. S-adenosyl methionine or SAM) can add methyl groups to DNA bases and produces transition mutations (G:C → A:T)
Induced DNA ramage results from
Chemicals that are mutagenic to replicating AND non-replicating DNA
Alkylating agents - mutagens that react with DNA bases and add methyl or ethyl groups and induce (directly or indirectly) transitions, transversions, frameshifts and chromosomal aberrations
Nitrous acid (HNO2) - deaminating agent, removes amino groups from A, C, and G, causes transition mutations (A:T to G:C)
Hydroxylamine - hydroxylates amino group of C and causes it to pair with A, leads to transition mutation (C:G → OHC:A → T:A)
Chemicals mutagenic to replicating DNA only
Base analogs - 5-bromouracil (resembles T) and 2-aminopurine (resembles A or G) can be incorporated into DNA during replication and later cause transition mutations through occurrence of rare tautomers
Acridines - intercalation of acridine dye (planar rings e.g. proflavine, ethidium bromide, acridine orange) into DNA structure causing frameshift mutation during DNA replication
Radiation-induced mutations
UV light induces mutations through excitation
X-rays and shorter wavelengths induce mutations through ionization
Mutagenesis by UV radiation produces cross-linking of adjacent thymines, making thymine dimers (covalent bond of pyrimidine rings)
Blocks DNA replication, can cause double stranded DNA breaks (serious issue)
At peak hour sunlight, each human skin cell exposed to sun acquires ~4500 thymine dimers/h
X-ray ionizing radiation can cause DNA strand breaks and changes in chromosomal structure
Causes nicks and DSB in chromosomes
Faulty repair of strand breaks by recombination can cause gross chromosomal rearrangements such as deletions, duplications, inversions and translocations
Direct reversal of DNA damage
Light-dependent repair - direct repair of thymine dimers (and other UV-induced photoproducts) by photolyase, also called photoreactivation, only found in prokaryotes
Enzymatic removal of alkyl groups from DNA bases (e.g. removal of methyl group from methylguanine so it returns to being just guanine and can pair with thymine)
Ligation of single-stranded nicks in DNA - occurs when there is a 5’ phosphate near a 3’ OH
Excision repair - base excision repair and nucleotide excision repair, same basic features:
Excision repair
DNA repair endonuclease which can recognize damage to DNA, bind to it and excise damaged DNA
DNA polymerase - fills in gap using undamaged complementary strand of DNA as a template
DNA ligase seals the break left by DNA polymerase
Base excision repair (BER) - specifically recognizes and repairs DNA bases damaged by deamination, alkylation or oxidation, found in both prokaryotes and eukaryotes
DNA glycosylase detects and removes damaged base, breaks glycosidic bond
DNA endonuclease recognizes apurinic site left by DNA glycosylase and cleaves phosphodiester bonds on either side, removing deoxyribose sugar
DNA polymerase adds new nucleotides, complementary to template strand
Phosphodiester bonds reformed by DNA ligase
Nucleotide excision repair (NER) - acts to remove thymine dimers and other bulky forms of DNA damage that block DNA replication
Mechanism is similar for prokaryotes and eukaryotes but eukaryotes have a more complex process with more proteins
Enzyme complex removes a short tract of DNA around mutation and resynthesizes it
Mutation of human NER genes causes xeroderma pigmentosum - cells cannot remove pyrimidine dimers and patient is prone to skin cancer
Mismatch repair
recognizes mismatched base in a newly-synthesized strand of DNA through ID of hemi-methylation GATC sequence
Recombination
Homologous recombination (HR) - occurs during or after DNA replication, if one sister chromatid suffers a DSB, it can be repaired using identical (unbroken) sister chromatid
HR also used to ensure proper chromosome separation (disjunction) during meiosis
Replication either stops or leaves a gap when encountering a pyrimidine dimer
If dimer occurs on leading strand side, lagging strand is synthesized normally
HR uses lagging strand as a template for leading strand gap caused by dimer
Pyrimidine dimer remains in the strand, must still be excised by NER or MMR
Non-homologous end joining (NHEJ) - different set of proteins to repair DSB, occurs throughout cell cycle, unlike HR which only occurs in S/G2 phases
Translesion synthesis
error-prone repair mechanism, uses TLS DNA polymerases
TLS DNA polymerases have lower fidelity of copying so they can replicate through damaged DNA, unlike normal polymerases which copy bulk of DNA in prokaryotes and eukaryotes
Pyrimidine dimers and other bulky DNA lesions block DNA pol. I and III, results in cell death
TLS DNA polymerase recruited to replicate through DNA damage, bypassing the lesion, and inserting random nucleotides in order to bypass it
TLS pol. swapped for pol. III once lesion is passed which properly copies rest of chromosome
Essentially TLS pol. Is a placeholder, but does cause mutations, is a last resort mech.
Some errors caused by TLS pol. can be fixed later by various DNA repair mechs.
SOS response - induced response to heavy mutation of bacterial chromosome which involves activation of DNA recombination, repair and replication proteins (including TLS polymerases)
In bacterial cells, an increase in mutation = possible adaptation
Eukaryotic cells have a similar response to damaged DNA
