Biochemistry - DNA Repair

Question 1

Permanent Mutations

Answer 1

Mutations will only become fixed in the genome when the DNA polymerases synthesize new daughter strands.

Question 2

exonuclease activity

Answer 2

Polymerases that hydrolyze DNA in the 3’ to 5’ direction (i.e., analogous to a ‘delete key’).

Question 3

Strand-directed Mismatch Repair (MMR)

Answer 3

Detects distortions in the DNA helix that result from a misfit between non-complimentary base pairs. Discriminates between mother and daughter strand; the presence of single strand breaks in newly replicated DNA appears to specify the strand to be repaired.

Question 4

General Steps of MMR

Answer 4

1) The Msh protein binds to a bulge (which indicates a mismatch) in the double-stranded DNA. 2) The Mlh protein then binds to Msh at the DNA and scans for the closest nick. 3) Once a nick is found, Mlh triggers the degradation of the nicked stand all the way back through to the mismatch. 4) The gap is then filled in by DNA polymerase and sealed by DNA ligase.

Question 5

Msh protein

Answer 5

binds to a bulge (which indicates a mismatch) in the double-stranded DNA.

Question 6

Mlh protein

Answer 6

Scans for the closest nick, then triggers the degradation of the nicked stand all the way back through to the mismatch.

Question 7

DNA glycosylases

Answer 7

Travel along the DNA helix to probe all faces of the nucleotide for damage. Cleaves the bond between the damaged base and deoxyribose, leaving behind an AP site. lesion specific, 8 different types.

Question 8

AP endonuclease

Answer 8

an enzyme that is involved in the DNA base excision repair pathway (BER). Its main role in is to create a nick in the phosphodiester backbone of the AP site created when DNA glycosylase removes the damaged base.

Question 9

Base excision repair

Answer 9

responsible for removing small, non-helix-distorting base lesions from the genome that could otherwise cause mutations by mispairing or lead to breaks in DNA during replication. It is initiated by DNA glycosylases, which recognize and remove specific damaged or inappropriate bases, forming AP sites. These are then cleaved by an AP endonuclease.

Question 10

Nucleotide Excision Repair (NER)

Answer 10

Recognizes structural distortions in the double helix such as pyrimidine dimers where 2 adjacent thymine (or cytosine) residues are covalently linked. Bulky lesions are removed from the strand with several additional nucleotides (‘oligonucleotide’), not just the damaged bases.

Question 11

Non-Homologous End Joining (NHEJ)

Answer 11

A non-homologous end-joining process can be used to “glue” double stranded DNA strands back together. Each broken strand uses the other as a template for DNA replication. DNA ligase seals the gap. Mutagenic ane error rone, b/c multiple base pairs are removed.

Question 12

Homologous Recombination (HR)

Answer 12

Repairs sdouble strand breaks during cell division when duplicated chromosomes have not separated. Ensures accurate repair by using the undamaged sister chromatid or homologous chromosome as a template.

Question 13

BRCA1 and BRCA2

Answer 13

proteins involved in double-strand DNA break repair. Mutations in these genes are inherited (hereditary). Women with heritable mutations are 40-80% more likely to develop breast cancer.

Question 14

Endogenous Sources of DNA Damage

Answer 14

1. DNA replication error 2. Deamination 3. Base Hydrolysis 4. Oxidation

Question 15

Exogenous Sources of DNA Damage

Answer 15

1. UV damage 2. Carcinogens: DNA adducts

Question 16

Deamination

Answer 16

The removal of an amine group. Will alter the structure of a base such that it now pairs with different partners during DNA replication. Repair: Base Excision Repair.

Question 17

Depurination

Answer 17

removal of a purine base from the DNA strand. The glycosidic bond between the purine base and sugar in a nucleotide can spontaneously hydrolyze leaving the ribose sugar without a base (creating an apurinic site). Repair mechanism: Base excision repair

Question 18

Reactive oxygen species

Answer 18

Metabolic byproducts that can damage the bases of DNA to cause mispairing, cause the complete loss of a base from a ribose residue, and induce single- and double-stranded breaks . ex: O2-, -H2O2, OH-. Repair: BER

Question 19

cyclobutane ring

Answer 19

Link between two adjacent thymine bases on the same strand as a result of UV light induction of pyrimadine dimer formation. Repair: NER.

Question 20

Xeroderma Pigmentosum (XP)

Answer 20

Hereditary inability to repair DNA damage that results from UV radiation because of defective NER mechanism. ~1000x greater risk of developing skin cancer and ~100,000x greater risk of developing carcinoma of the tip of the tongue.

Question 21

DNA Adducts

Answer 21

a piece of DNA covalently bonded to a (cancer-causing) chemical.

Question 22

Carcinogens

Answer 22

Cancer-causing agents that can react with DNA bases, often adding bulky adducts to DNA (Ex: benzopyrene). other examples: acetaldehyde–occurs naturally; and also a major constituent of tobacco smoke; Heterocyclic amines, which form as the result of cooking foods at high temperatures (most notably red meat), can form similar adducts. Repair: NER, adduct too bulky for BER.

Question 23

Nucleotide Excision Repair fixes:

Answer 23

ss Break, link betwene adjacent bases, DNA adducts

Question 24

Base Excision Repair fixes:

Answer 24

Deaminated base, oxidized base, missing base.

Question 25

hereditary nonpolyposis colorectal cancer

Answer 25

DNA mismatch repair, caused by irradiation or chemical mutagens, affecting the colon or ovary. Early tumor development.