DNA Repair

Name the 2 important tumor suppressor genes involved in DNA Repair.

1. Brca1 2. Brca2 mutated in inherited breast and ovarian CA

Name the 5 major pathways of repair.

1. Mismatch Repair (MMR) 2. Base Excision Repair (BER) 3. Nucleotide Excision Repair (NER) 4. Homologous Recombination (HR) 5. Non-Homologous End Joining (NHEJ)

Identify the 2 subtypes of Nucleotide Excision Repair.

1. Transcription Coupled Repair 2. Global Genome Repair

Genetic Anticipation, based on the number of trinucleotide repeats found in the DNA, can account for what 3 variations in disease?

1. increased odds of inheriting 2. decreased age of onset 3. increased severity in later generations

What is the most common type of oxidized base formed from Oxidative Damage to Nucleotides.

8-hydroxyguanine base pairs with A instead of C

What type of damage is Nucleotide Excision Repair responsible for repairing?

either covalent attachments of large hydrocarbons on nucleotides OR Pyrimidine Dimers

Loss of imprinting or overexpression of imprinted genes is caused by what?

global hypomethylation

Does Global Genome Repair occur more or less often in a terminally differentiated cell?

occurs LESS often

What specific methylation patterns are seen in cancer?

overall HYPOmethylation in the DNA, expressing genes not normally expressed HYPERmethylation of promoter regions of genes encoding tumor supressors and caretaker proteins- less are transcribed/translated

The cleavage and rejoining of DNA in Homologous Recombination repair mechanism is said to be inaccurate or precise?

precise occurs using sister chromatids in S or G2 phase

In what region of the gene is a trinucleotide repeat found in Fragile X syndrome?

promoter region

When MMR protein finds small structural distortion on newly synthesized strand of DNA, what happens to repair the damage?

region between damage and subsequent nick is removed from the newly synthesized strand. DNA polymerase comes in to fill the gap DNA ligase seals the nick

In a patient with Huntington's disease, MMR pathway is intact but does not repair TNR expansion due to what?

secondary structure of DNA in a SPECIFIC GENE

The CpG island methylator phenotype (CIMP) is characterized by what phenomenon?

widespread promotor hypermethylation present in ~18% cases of colorectal cancer

What repair pathway repairs damage caused by either Deaminated Cs or As, Damaged Nitrogenous Bases (Depurination), Alkylated or Oxidized bases, bases with open rings or bases with reducible double bonds?

Base Excision repair DNA glycosylase recognize specific types of damage and catalyzes removal (excision) of the damaged nitrogenous bases by hydrolysis of the N-glycosidic bond [leaves sugar backbone intact]

The favored model to describe trinucleotide expansion is 'Slippage.' Describe Slippage.

Because repeats are rich in G-C pairs and have a tendency to form hairpin loops, the newly synthesized lagging DNA strand in a trinucleotide repeat region can form a hairpin loop, pull DNA polymerase backwards and copy the same region of DNA twice -> doubles/expands the trinucleotide region already present

If telomerase is reactivated in a cell containing DNA caught in the breakage-fusion-bridge cycle, what will result?

CANCER - lengthen telomeres of damaged chromosomes - making them immortal

DNA repair proteins can be classified as either tumor suppressors or a class of their own known as what?

Caretakers

Why can't Hypermethylation of CpG islands be the first hit in inherited forms of cancer?

DNA methylation patterns are erased during gametogenesis

In NHEJ, Ku-Kinase-Nuclease complex unwinds strands, finds small region of homology where it can base pair the strands together then what occurs prior to ligation of [hopefully] repaired DNA?

Ends are trimmed, causing deletions causing further deletions after a double stranded break makes NHEJ an ERROR PRONE mechanism

Toxic-gain-of-function is the disease causing mechanism related to trinucleotide repeats in what part of the gene?

Exons! part actually coding for proteins

What structures on sister chromatids prevent fusion of DNA together?

Telomeres

What term is used to describe the fact that the same genetic disorder can be caused by mutations in different genes?

Locus Heterogeneity

What defect is present with microsatellite instability in many cancers?

MMR defect; either inherited as in Lynch syndrome or due to a mutation/methylation of genes encoding MMR proteins

What do we call short, tandem repeats of 4-6 nucleotides in DNA?

Microsatellites

When trinucleotide expansion occurs on a specific gene in Huntington's Disease, what un-damaged DNA repair mechanism SHOULD fix this problem but chooses not to?

Mismatch Repair

Lynch Syndrome is a genetic mutation in a major enzyme involved in which repair pathway?

Mismatch Repair ~3% colorectal cancers

Which repair pathway repairs polymerase error (mismatched bases) and small insertions or deletions?

Mismatch Repair! maintains stability of microsatellites

What general phenotype is observed when there is a DNA repair defect?

Mutator Phenotype

Decreased Transcription and RNA gain-of-function are disease causing mechanisms related to trinucleotide repeats in which region of genes?

Non-coding regions Lg changes in rpt # associated with maternal transmission

Xeroderma Pigmentosum, a rare genetic disorder, is a defect in which DNA repair pathway?

Nucleotide Excision Repair unable to repair UV induced damage, increased risk of CA 1000X

What is the difference between the result of HR in mitosis versus meiosis?

REPAIR of double stranded break in mitosis leads to new DNA synthesis on damaged chromosome ONLY Chromosome mixup for variation in meiosis leads to new DNA synthesis on both chromosomes (crossover)

What is the term that describes RNA interfering with function of protein involved in mRNA processing?

RNA gain-of-function

What is Depurination?

Spontaneous loss of an Adenine or Guanine nitrogenous base

What is the event during transcription recognized by repair proteins that alerts the cell to the necessity of Transcription Coupled Repair?

a stalled RNA polymerase when it senses damage on DNA template strand

MSI+ tumors are more genetically stable making them tumors with a better or poorer patient prognosis?

better prognosis! DNA is stable- easier to fix than out of control DNA

What occurs when chromatin structure is changed or methylation is increased? This can lead to disease.

decreased transcription

In a patient with lynch syndrome, microsatellite length changes are not repaired due to what?

defect in MMR pathway

Hypermethylation of CpG islands in cancer is termed what?

Abnormal Gene Silencing

What is the difference between the Deamination of Cytosine versus the deamination of methylated Cytosine?

Deaminated Cytosine = Uracil -> detected as damage and is repaired! Deaminated methyl Cytosine = Thymine (supposed to be in DNA) -> more difficult to recognize as damaged The fact that deamination is so common and methyl Cytosine is more common than Cytosine in the genome is why CpGs are underrepresented!

Name the type of DNA damage that results in unusual bases not normally found in DNA from common, spontaneous loss of an amine group (NH2).

Deamination

What is the result of Depurination if it is not repaired?

Deletion

Why does Non-Homologous End Joining repair double stranded breaks only in the G1 phase of the cell cycle?

Does not require sister chromatid produced in replication during S or prior to mitosis in G2

Which base pairs are stronger? GC or AT?

GC are stronger - regions rich in GC are more likely to form hairpin loops

What 2 types of repair pathways will come into play in the case of a double strand break?

Homologous Recombination (S or G2 phase) or Non-homologous End Joining (G1 phase)

How is Toxic Gain-of-Function different from RNA gain-of-function?

Toxic gain-of-function involves PROTEINS interfering with the jobs of other proteins RNA gain-of-function involves RNA interfering with the jobs of proteins

How does a chromosome enter the breakage-fusion-bridge cycle?

When a chromosome without a telomere is replicated- fuses to sister chromatid, has to break somewhere during mitosis and will produce another chromosome without a telomere

In nucleotide excision repair, removal of the damaged section of the DNA strand is double excised then unwound and removed by what enzyme?

the helicase function of TFIIH