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Classes of mutations

Transitions- one base to another of the same

Transversions- one base replaced by the opposite

These can lead to silent, nonsense, and missense mutations

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Specific types of mutations

Slent- no effect in the protein

Nonsense- early stop codon

Missense- change in the amino acid that the codon codes for

Frame shift- bases lost or gained. Polymerase might slip and skip a base or sometimes old strand being replicated will bubble up and an extra base will be inserted

Most mutations are neutral, no affect n organism- don't matter in somatic cells

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Failure to correct lesions can lead to mutations

Mutations in cells that form gametes will be passed on to progeny (diseases or phenotypic differences)

Mutations in cells that do not form gametes (somatic cells) can interfere with gene expression or replication, lead to formation of tumors and cancers, or speed up aging

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Although mutation has a bad connotation, it isn't all bad

Ultimate source of genetic variation

Can either have deleterious or advantageous outcomes for an organism

Intentional mutations are a powerful tool in molecular biology

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Thymine-dimer formation

Direct damage by UV-B lighting.

Thymines form a dimer. Causes a bulge/legion, bumpy region in DNA. It'll look different to a protein

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Nucleotide excision repair

Recognizes and removes bulky regions

Similar repair pathways found in all organisms, from bacteria to humans

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Two pathways of nucleotide excision repair

Global repair pathway- proteins are scanning the entire genome- XPC recognizes the region

Transcription coupled pathway- only scanning DNA that is being transcribed

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Nucleotide excision repair process

Recognition of lesion (two pathways)

DNA is denatured and the strands are separated, creating a bubble

TFIIH recruited, nick on either side

Excision of ssDNA

DNA synthesis (DNA polymerase delta and epsilon)

Ligation

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Base excision repair

Removal of chemically modified bases

Only modified base removed

Mnt different enzymes that recognize specific common mutations have been identified
-Deaminated C to uracil
-8 hudroxyguanine
-3 methyladenine
-deaminated 5-methyl C

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Deamination of cytosine

Hydrolysis of amino group from cytosine

Happens spontaneously, generating uracil in the DNA

Uracil base pairs analogously to thymine, which will lead to a GC to AT change after replication if not corrected

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Base excision process

Group of enzymes (glycosylases) recognizes chemically modified bases. Pulls out the base.

Endonuclease cut in the middle of the strand(nicks sugar phosphate backbone)

DNA polymerase beta comes in and removes the other phosphate and inserts the correct base.

DNA ligase seals it

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DNA mismatch repair

Errors during replication that escape the proof reading function of DNA polymerase

Nucleotide excised from new strand of DNA in addition to additional bases and replaced

Problem- which one is parent strand? To fix the error.. New vs old strand detected in different ways in eukaryotes and prokaryotes (unknown in euk)

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Mismatch excision repair process

Mismatch occurs, correct base is on the parental (methylated strand), incorrect base on newly synthesized (unmethylated) strand- Parental strand is methylated so the repair enzyme knows which base is correct

Enzymes detect the mismatch and cut the unmethylated strand

DNA polymerase I excises nucleotides on the unmethylated strand

DNA polymerase I fills in the gap in the 5'-3' direction

DNA ligase links the new and old nucleotides

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Double strand breakage repair- NHEJ

Ionizing radiation can break both strands of the double helix

NHEJ- non homologous end joining

Proteins recognize the breaks and join to the ends and bring in enzyme that joins the bits together. Ligase. However base pairs are lost in this process (more than one or two). Bad if in coding region

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Homologous DNA repair

Nucleolytic processing leaves a 3' overhang that is coated by RAD51

BRCA1/2 recruits repair factors, creates overhangs. Ssb proteins stabilize overhangs on broken strand of DNA. (loss of function of these proteins tends to induce cancer in the mammary or ovarian epithelial cells)

One of the RAD51 coated nucleoprotein filament searches for the homologous duplex DNA sequence in the sister chromatid

3' end is elongated by DNA polymerase, then base pairs with other damaged strand with the 3' overhang

DNA polymerase and ligase fill in the gaps

Error free

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Diseases

Xeroderma pigmentosum

Cockayne syndrome

Huntington's disease

Fragile x syndrome

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Xeroderma Pigmentosum

Deficient nucleotide excision repair that cannot repair damage done by UV radiation

Exposure to sunlight can produce spots on the affected areas

Can develop fatal skin cancers

DNA repair enzymes in skin creams

UV light creates kinks that cannot be repaired

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Cockayne syndrome

Cockayne syndrome B protein

CSB essential for repair mechanisms coupled with transcription, and for starting transcription after repair has occurred occurred after exposure to UV light

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Huntington's disease

Tri nucleotide repeats

Autosomal dominant neurodegenerative disorder

Gene found on chromosome 4

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Tri nucleotide expansion: error in replication

In DNA replication dna melts, and renneals improperly or Polymerase can skip or stall causing a bulge behind it

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Trinucleotide repeats: unequal crossing

Microsatellites, crossing over

Homologs pair up, repeats misalign, crossing over and recombination occurs. Products are unique

Longer satellite bigger chance

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Fragile X

Length of repeat is associated with the severity of the condition

Eventually there is a break

Maternally inherited