Lecture 13

Question 1

What are three excision repair pathways that exist to repair single stranded DNA damage?

Answer 1

Nucleotide excision repair (NER), base excision repair (BER), & DNA mismatch repair (MMR)

Question 2

What is nucleotide excision repair?

Answer 2

Nucleotide excision repair (NER) is a particularly important excision mechanism that removes DNA damage induced by ultraviolet light (UV). UV DNA damage results in bulky DNA adducts - these adducts are mostly thymine dimers and 6,4-photoproducts. Recognition of the damage leads to removal of a short single-stranded DNA segment that contains the lesion. The undamaged single-stranded DNA remains and DNA polymerase uses it as a template to synthesize a short complementary sequence

Question 3

What is base excision repair?

Answer 3

A cellular mechanism that repairs damaged DNA throughout the cell cycle. It is responsible primarily for removing small, non-helix-distorting base lesions from the genome. BER is important for removing damaged bases that could otherwise cause mutations by mispairing or lead to breaks in DNA during replication.

Question 4

What is DNA mismatch repair?

Answer 4

DNA mismatch repair is a system for recognizing and repairing erroneous insertion, deletion, and mis-incorporation of bases that can arise during DNA replication and recombination, as well as repairing some forms of DNA damage.

Question 5

What is photolyase?

Answer 5

Photolyases are DNA repair enzymes that repair damage caused by exposure to ultraviolet light.

Question 6

What is an alkyl-transferase?

Answer 6

Alkylated DNA is directly repaired by enzymes known as alkyltransferases

Question 7

What are examples of extrinsic mutagens?

Answer 7

UV light, ionization radiations (x-rays), chemicals, cultural artifacts (cooking & smoking), & natural food carcinogens

Question 8

What are examples of intrinsic mutagens?

Answer 8

Heat (deamination & depurination), oxygen radicals & reactive metabolites

Question 9

What is the Ames test?

Answer 9

The Ames test is a widely employed method that uses bacteria (Salmonella) to test whether a given chemical can cause cancer. More formally, it is a biological assay to assess the mutagenic potential of chemical compounds. A positive test indicates that the chemical is mutagenic and therefore may act as a carcinogen, because cancer is often linked to mutation. His- –> His+ reversion (back mutation) is indicator

Question 10

How common is DNA damage (in terms of events per human per day)?

Answer 10

Depurination is most common (10^18), while Deamination and Oxidation occur fairly equally (5x10^16)

Question 11

What are three DNA damage repair pathways?

Answer 11

Excision repair (Nucleotide Excision Repair, Base Excision Repair, DNA Mismatch Repair), Non-excisive repair (no cutting of DNA; “Direct Repair”), & DNA Double-Stranded Break (DSB) repair

Question 12

What are methods of DNA damage avoidance?

Answer 12

1) Detoxification of oxygen radicals and alkylating agents

2) Hydrolysis of damaged dNTPs to prevent incorporation

Question 13

What is Cockayne syndrome (CS)?

Answer 13

Cockayne syndrome is a rare autosomal recessive, congenital disorder characterized by growth failure, impaired development of the nervous system, abnormal sensitivity to sunlight (photosensitivity), and premature aging. Loss of CS-A or CS-B (or certain partial defects in XPB, XPD or XPG) leads to Cockayne syndrome. The proteins made by these genes are involved in repairing damaged DNA via the transcription-coupled repair mechanism, particularly the DNA in active genes. Little skin cancer

Question 14

What is Trichothiodystrophy (TTD)?

Answer 14

Trichothiodystrophy (TTD) is an autosomal recessive inherited disorder characterized by brittle hair and nails, intellectual impairment, and UV sensitivity. It is caused by defective XPB or XPD (helicase components of transcription/repair factor TFIIH). No cancer predisposition

Question 15

What is Xeroderma pigmentosum (XP)?

Answer 15

Xeroderma pigmentosum, or XP, is an autosomal recessive genetic disorder of DNA repair (nucleotide excision repair) in which the ability to repair damage caused by ultraviolet (UV) light is deficient. In extreme cases, all exposure to sunlight must be forbidden, no matter how small; as such, individuals with the disease are often colloquially referred to as Children of the Night. Patients with XP die early of multiple cancers

Question 16

Why can a defect in XPD lead to XP, TTD, or CD?

Answer 16

Different types of defects in XPD lead to differential effects on repair and transcription, leading to different phenotypes

Question 17

What are two types of non-excisive repair?

Answer 17

Photolyase (photoreactivation) & DNA Alkyl transferases

Question 18

What are two types of DNA double-stranded break (DSB) repair pathways?

Answer 18

Homologous recombination & Non-homologous DNA End Joining

Question 19

What is Non-homologous end joining (NHEJ)?

Answer 19

NHEJ typically utilizes short homologous DNA sequences called microhomologies to guide repair. These microhomologies are often present in single-stranded overhangs on the ends of double-strand breaks. When the overhangs are perfectly compatible, NHEJ usually repairs the break accurately. Imprecise repair leading to loss of nucleotides can also occur, but is much more common when the overhangs are not compatible. Inappropriate NHEJ can lead to translocations and telomere fusion, hallmarks of tumor cells.

Question 20

What is Bloom syndrome?

Answer 20

Bloom syndrome is an autosomal recessive disorder characterized by growth defects, sun-sensitivity, skin pigmentation, chromosomal instability, male infertility (females are sub-fertile), & cancer predisposition. It is caused by defective BLM (Bloom gene) coding for a RecQ-like helicase. This causes defect in recombination, including DSB repair.

Question 21

What is Werner syndrome?

Answer 21

Werner syndrome is an autosomal recessive disorder characterized by cancer predisposition, premature aging, chromosomal instability, and other age-related diseases such as osteoporosis, atherosclerosis, cataracts, diabetes, premature graying, and loss of hair. It is caused by defective WRN coding for a RecQ-family helicase, however the WRN protein is unique in having both helicase and nuclease activities. Therefore, there are defects in recombination, including DSB repair.

Question 22

How does a defect in XPD lead to XP, TTD, or CS?

Answer 22

It depends on where the defect occurs along the XPD gene. Different defects result in different levels/efficiencies of transcription

Question 23

What do Polymerases Iota and Zeta do?

Answer 23

If depurination occurs without DNA repair, polymerases iota and zeta will replace the missing bases with new nucleotides. This prevents a frame shift mutation in the reading frame

Question 24

What does polymerase Eta do?

Answer 24

Polymerase Eta inserts AA opposite a TT dimer caused by UV radiation. This restores the replication

Question 25

What is Xeroderma Pigmentosum Variant (XPV)?

Answer 25

Patients suffer hypermutagenesis because they lack Polymerase Eta. These patients die early of multiple cancers