DNA Repair – Vocabulary Flashcards

Vocabulary flashcards derived from the DNA Repair lecture notes.

DNA Mutation

A permanent change in the nucleotide sequence of DNA.

Substitution Mutation

Replacement of one base pair with another.

Insertion Mutation

Addition of one or more base pairs into the DNA.

Deletion Mutation

Deletion of one or more base pairs from the DNA.

Silent Mutation

Mutation that affects nonessential DNA or has negligible effect on gene function.

DNA damage causes

Inhaled chemicals, ingested chemical from carcinogens, UV rays, ionizing radiation (x-rays), free radicals from the ETC or other cellular processes, mutations, and spontaneous changes to existing DNA

Direct Repair

Repair pathway that directly reverses specific DNA damages, via photolyases or methyltransferases.

Photolyase

Enzyme that uses light energy to repair pyrimidine dimers (via FAD) in some organisms. (i.e. fixes T=T bonding)

O6-methylguanine-DNA Methyltransferase

Direct repair enzyme that transfers the methyl group from O6-methylguanine to its own cysteine residue, inactivating itself and regenerating guanine using folate.

Mismatch Repair

Corrects base-pair mismatches using template strand information; in bacteria the template strand is distinguished by methyl tags. Enzymes start up/ downstream of mutation; fills in removed, mismatched segment using methylated template.

Base Excision Repair

Removes damaged bases with DNA glycosylases, creates an AP (apurinic/ apyrimidinic) site with an OH left behind. Then AP endonuclease cuts and flips it to the outside, and DNA polymerase fills with new DNA; ligase seals.

Nucleotide Excision Repair

Repairs lesions causing large DNA distortions using an endonuclease (excinuclease) to remove a short (12-13 bases/ 27-29 bases in euk.) DNA segment, followed by filling via polymerase and ligation.

Uracil DNA glycosylases

removes uracil that results from spontaneous deamination of cytosine, preventing incorrect pairing of U and A

Hypoxanthine DNA glycosylases

remove hypoxanthine that results from adenine deamination, preventing H - C pairing

Chromatin

Tightly coiled DNA; accessibility regulated by binding tightness

Histone proteins

Have positively charged residues that associate with DNA; includes H2A, H2B, H3, and H4; 150bps wrap around each core, and H1 wraps around each core

Euchromatin

Less dense version of chromatin; makes up 90% of chromatin

Heterochromatin

Heavily condensed version of chromatin (like during mitosis); makes up 10% of DNA

Histone N tails

Lysine tails can be acetylated and methylated; arginine tails can be methylated; serine tails can be phosphorylated

Acetylation

Modification that causes lysine to become neutrally charged, reducing attraction between histone proteins and DNA, causing it to loosen and be more transcriptionally active

Deacetylation

Enzymes that remove acetyl groups from lysine residues on histone tails, causing them to become positively charged again and interact more strongly with histone proteins, decreasing transcriptional activity

Methylation

Modification that can activate or repress transcription, depending on which AA is modified and how many methyl groups are added. May or may not influence charge

histone code

The idea that different chemical modifications are used in conjunction in a specific way that dictates whether translation is activated or repressed. This recruits certain proteins that alter chromatin structure to activate or repress transcription

Chemical modifications to DNA - DNA methylation

In eukaryotes, occurs on Cyt residues, which represses transcription through interfering of binding with transcription factors or through recruiting inactivating proteins

nucleosome remodeling factors

Proteins that can influence chromatin structure without chemical modifications. Can reposition nucleosomes by sliding along DNA, freeing up stretches to be transcribed. Others can facilitate binding of transcription factors