Flashcards in Lectures 24+25 Deck (38):
What is mutation rate (Greek letter mu)?
mu = n/2N where n is the number of affected offspring from unaffected parents and N is the total number of offspring. This describes the number of new mutations per generation.
What is the ultimate source for genetic variability?
In a temperature sensitive mutant, what is affected?
The gene, the encoded mRNA, and the protein are all mutant.
What is the most common type of mutation in genetic disease?
What is exact genetic reversion, and how often does it occur?
Exact genetic reversion is when a gene mutation is reverted back to exactly what it was before, and it is VERY rare.
What is Equivalent Genetic Reversion?
It is when a subsequent mutation restores function from the initial mutation. Because there's redundancy in codons, if the initial (forward mutation) changed a codon from GAG (Glu) to GTG (Val) and the subsequent mutation (reverse mutation) change the GTG (Val) to GAA (Glu), function would be restored even though it's not the exact same codon as the original GAG.
How does "Suppression" work to overcome mutation?
A compensating 2nd site mutation restores, at least partially, the functionality lost from the 1st mutation.
What are the 2 types of Suppressor mutations?
1. Intragenic - a 2nd compensating mutation in the
same reading frame restores some function
2. Extragenic - a 2nd compensating mutation that
occurs in another gene/reading frame restores partial function --> typically observed when the 1st mutation disrupts the interaction between two proteins and the
2nd compensating mutation helps to restore that
When phenotypic reversion is observed, what is the more likely underlying reason?
The more likely underlying cause is a Suppressor mutation, rather than a genetic reversion.
What is somatic mosaicism and how might it happen?
Somatic mosaicism is when phenotypically reverted cells are conferred some competitive advantage, and can outgrow the non-reverted cells. This can sometimes be seen in skin conditions where the reverted cells survive better, and thus outgrow the mutant cells (i.e. Epidermolysis with somatic mosaicism.)
What are the 4 checks for Polymerase errors on normal DNA templates?
1. Polymerase selectivity characterized by "ternary complex."
2. Ploymerase proofreading
3. Post-replication mismatch repair
4. Collection of repair and error-avoidance mechs
How does polymerase selectivity work?
It is thought that polymerase undergoes a conformational change at its catalytic site such that only the complementary base to the one it reads on the template strand can be added.
What is the key feature of DNA polymerase that allows it to "proofread?"
It has 3' --> 5' exonuclease activity that allows it to correct a mismatched base pair, but this MUST happen within 2 NTs or less of the error. Otherwise, the error can not be corrected by proofreading.
How does that "dam" mismatch repair work and how does the machinery know which DNA strand is the nascent strand?
If a mismatch occurs within 20-2,000bp of a DAM site with sequence GATC, MutL/H/S will nick the unmethylated DNA strand (the nascent strand) at the GATC site and helicase with endonuclease act at the nick site to create a gap starting from the nick, ending at the mismatch. Finally, DNA Pol fills in the gap.
Which of the 3 Fidelity mechanisms provides for the highest order of fidelity?
Polymerase selectivity, which has an approximate error rate of 10^-5. The other 2 mechs are 10^-2
What is HNPCC (Lynchman Syndrome) brought on by, and what are the symptoms?
It is an autosomal dominant disease brought about by defective MISMATCH REPAIR genes. It causes a predispositon to colon cancer.
How does misreplication occur at repetitive sequences?
DNA breathing (when polymerase stalls and briefly dissociates from the DNA) allows "strand slipping" such that the repetitive sequence can slip forward or backward, so the new strand will have more or fewer NTs.
What is the most important/deleterious mutation caused by O2 radicals?
8-oxoguanine is the most mutagenic. It pairs with A because its mutation causes it to "rotate" and form a Hoogstein Pairing.
What is considered to be the most important/frequent source of DNA damage in humans and what is it characterized by?
rNTPs (ribonucleotides) inserted into DNA. rNTPs can be inserted instead of dNTPs because both are present in the cell. The wrongful insertion of rNTPs potentiates breaks or "nicks" in the DNA, because there are enzymes that scan specifically for this error. These breaks/nicks must then be repaired.
What is an example of a disease caused by a transposable element disrupting gene function?
How does the Ames test work
His- bacteria are introduced to an agar gel without His and a test substance is added to one of the gels while the other gel has just the His- bacteria (control.) If bacterial colonies grow on the His- gel to which the test sample was added, the test sample must have caused a reversion mutagenesis to allow the bacteria to produce His and thus grow.
What is one of the most common types of DNA damage called that leads to an abasic site?
Depurination --> leads to abasic site
What are the two types of excision repair mechs?
NER (nucleotide excision repair) and BER (Base excision repair.)
How to NER and BER differ?
Ner begins by cleaving the damaged DNA strand and creates a gap of about 12-30 NTs, whereas BER begins by cleaving the glycosyl bond of the mismatched/damaged NT and leaves a gap of about 1-2 NTs
What does Aicardi Goutieres syndrome arise from?
It arises from an issue with RER (Ribonucleotide Excision Repair) gene RNaseH2, which is a very important repair mech seeing as the majority of DNA damage comes from accidental insertion of rNTP into the nascent DNA strand.
What is Transcription-Coupled NER?
It is a type of NER that happens faster than in non-actively transcribed DNA, because some of the factors (XPD and XPB for example - components of transcription factor TFIIH) are involved in both transcription and NER. So, recruitment of NER factors occurs much faster during transcription because some are already present.
Why can you get different types of diseases from mutations within the same protein, for example mutations in XPD, and what are the diseases that arise from mutations in XPD?
Because XPD has multiple functions, both in transcription and in NER, depending on which domain the issue is in, you can see different phenotypic expressions. If the issue is in its NER domain, then Xeroderma Pigmentosum results. If the issue is in its transcriptional domain, you could observe TTD (Trichothiodystrophy or Cockayne Syndrome.)
What are some examples of DNA repair mechs other than NER and BER?
Non-excision repair and Double Stranded Break (DSB) repair
What are the steps involved in DSB repair for non-homologous end joining?
1. "End protection" --> proteins cap the 2 ends where the breaks occurred.
2. "End Juxtaposition" --> the cap proteins bring the two ends together-ish
3. The DNA ends are joined either with or without endonuclease activity (processing.)
What are some diseases that arise from issues with non-homolgous DSB repair?
Bloom Syndrome and Werner Syndrome
What are the characteristics of Bloom syndrome, and what is its root cause?
It is an autosomal recessive disease characterized by sun-sensitivity, skin pigmentation, chromosomal instability --> leads to Harlequin chromosome appearance (excessive recombination), and a few other things including predisposition to cancer. It is caused by an issue with the BLM gene that codes for RecQ-like helicase.
What are the characteristics of Werner syndrome and what is it the root cause?
Werner syndrome is characterized by progeroid symptoms/phenotype, and it is caused by an issue with the WRN gene that codes for a RecQ family helicase.
What is the characteristic symptom of Li-Fraumeni syndrome, and what pathway is affected?
Li-Fraumeni is characterized by heterozygosity for p53, and it leads to a very high predisposition to cancer. The pathway affected is the DNA damage response pathway mediated by p53.
What is the result of 6-methylguanine DNA damage?
Typically G compliments with C, but 6-methylguanine complements with T --> you end up with a GC:AT transition.
What issue does DNA Pol eta deal with?
DNA Pol eta is able to add AA complements to TT dimers, whereas other DNA Pols cannot transcribe when they reach a TT dimer.
What are the symptoms of XPV (XP Variant), and which pathway is affected?
XPV has the same phenotypic expression as XP (early skin cancers), but the issue here is not with NER. Instead, XPV affected individuals lack DNA Pol eta, so they cannot transcribe when TT dimers arise.
What are the characteristic symptoms of Cockayne syndrome and which pathway is affected?
Cockayne syndrome is characterized by neurodevelopmental issues, and the affected pathway is Transcription-Coupled(TC) NER/transcription.