Lecture 24

Question 1

quality control

Answer 1

• DNA is subjected to a huge array of chemical, physical, and biological assaults on a daily basis
• repair of damaged DNA is critical for maintaining genomic integrity and thereby preventing the propagation of mutations either horizontally (somatic cells) or vertically (germ cells)
• DNA damage typically halts the cell cycle in G1 until DNA repair

pg 576

Question 2

DNA repair overview

Answer 2

• replication is very accurate
• DNA repair is the primary reason for the accuracy -> takes place in all higher organisms
• several dozen enzymes involved in repair of damaged DNA
• enzymes recognize an altered base, excised it by cutting the DNA strand, replace it with the correct base, reseal the DNA
• DNA repair is essential for the accurate replication of DNA, defects in DNA repair systems can lead to many types of disease

pg 577

Question 3

types of DNA damage

Answer 3

endogenous

• internal factors

exogenous

• outside influences
• ionizing radiation
• chemotherapy
• oxidative free radicals
• chemotherapy
• viral infection

pg 578

Question 4

DNA damage response

Answer 4

1. damaged DNA strand
2. excision of damage
3. DNA polymerase makes repair
4. DNA ligase seals nick

pg 579

Question 5

five major DNA repair pathways/systems

Answer 5

• ionizing radiation, X-rays, anti-tumor drugs -> double strand breaks, single strand breaks, intrastrand crosslinks -> non homologous end joining (NHEJ) and homologous recombination (HR)
• UV-light, chemicals -> bulky adducts, pyrimidine dimers -> nucleotide excision repair (NER)
• oxygen radicals, hydrolysis, alkylating agents -> abasic sites, single strand breaks, 8-oxoguanine lesions -> base excision repair (BER)
• replication errors -> bases mismatch, insertions, deletions -> mismatch repair (MMR)

pg 580

Question 6

mismatch repair (MMR)

Answer 6

• correcting the mismatches of normal bases that either fail to maintain normal pairing or have insertions/deletions of one or a few nucleotides
• DNA mismatch -> repair proteins -> removal of newly synthesized strand -> DNA polymerase and ligase repair

pg 582

Question 7

base excision repair (BER)

Answer 7

• spontaneous depurination and depyrimidation
• goal of BER: to repair bases with foreign molecules attached OR depurinated/depyrimidated nucleotides
• DNA glycosylase removes the damaged base, leaving an open AP site
• AP endonuclease cuts out depurinated or depyrimidated nucleotide completely
• standard DNA replication machinery fills the gap

pg 584

Question 8

nucleotide excision repair (NER)

Answer 8

• remove UV light-induced damage as well as DNA damage from chemicals
• UV light can form pyrimidine-pyrimidine dimers (usually thymine)
• necessary to recognize chemically indused bulky additions to DNA that distort the shape of the DNA double helix and cause mutations
• 30 genes required for NER

pg 587

Question 9

how UV light damages DNA

Answer 9

• distorts structure of DNA
• can lead to stalled DNA polymerase if not repaired prior to replication -> leading to errors in replication
• can also impair transcription

pg 588

Question 10

double stranded DNA repair

Answer 10

• damage from ionizing radiation, oxidative free radicals, or chemotherapeutic agents causes both the strands of DNA to be severed
• two types of repair mechanisms exist to correct the damage: HR and NHEJ

pg 589

Question 11

double stranded DNA breaks

Answer 11

overall basic mechanism for repairing double stranded DNA breaks

• repair takes advantage of sequence information available from the unaffected homologous chromosome for proper repair of breaks
• sister chromatids used as templates for repair
• the “bad” strand invades the “good” strand to get sequence info
• “good” strand remains unaltered
• can result in gene conversion
• only during S and G2 phases

pg 590

Question 12

homologous recombination (HR)

Answer 12

• physically separated homologous chromosome used as a template
• “good” and “bad” strands mutually invade each other -> holiday junction
• can result in gene conversion or crossing over
• only during S and G2 phases

pg 592

Question 13

non-homologous end-joining (NHEJ)

Answer 13

• can occur in any stage of cell cycle or in non-dividing cells
• does NOT use homologous sequences to guide repair
• error-prone, but only affects individual cells (not passed on)
• tries to stick two pieces of DNA back together, but entirely posisble to stitch two “wrong” pieces of DNA if there are multiple double-stranded DNA breaks in the cell
• 4 enzymes used - Ku70/80, DNA-dependent PK, ligase IV, and XRCC4

pg 594

Question 14

big picture of DNA damage response

Answer 14

• three general components: sensors, transducers, effectors
• effectors fall into major categories: DNA repair, cell cycle arrest, apoptosis/senescence

pg 595-597

Question 15

human diseases of DNA damage repair

Answer 15

• defective NHEJ: SCID
• defective HR: Nijmegen breakage syndrome, Bloom syndrom
• defective NER: xeroderma pigmentosum
• defective BER: MAP
• defective MMR: hereditary nonpolyposis colorectal cancer (Lynch syndrome)
• all discussed in next lecture

pg 598