DNA Recombination, Repair

Question 1

Transitions

-base substitution-

Answer 1

Purine with a purine (A = G)

pyrimidine with a pyrimidine (C=T)

Question 2

Transversions

-base substitutions-

Answer 2

purine with a pyrimidine

alters geometry and change diameter:

2 single rings or 2 double rings

Question 3

Causes for sequence change and DNA damage

(6)

Answer 3

1. DNA Polymerase errors
2. Chemical modifications to bases

• spontaneous deamination (C → U) & depurination due to instability of purines → abasic sugar residue
• accelerated by nitrous acid (A → hypoxanthine, which bp w/ C) or hydroxylamine
• alkylating agents: methylation favors certain tautomer (dimethylsulfate, nitrogen mustard, dimethylnitrosamine, SAM)

3. Radiation damage by UV or x-ray light

• favors rare tautomeric form of bases (A→C)
• formation of free radicals
• activation of ethylene bonds of pyrimidines covalent link distorts DNA structure

4. Intercalating agents stretch double helix and cause addition of extra bases
   * ethidium bromide
5. System of DNA repair becomes error prone
6. Insertions and deletions caused by movable genetic elements

Question 4

Base excision repair (3)

Answer 4

*Removal of uracil (product of cytosine deamination)

1. Uracil DNA glycosylase hydrolytically removes base leaving a deoxyribose reside
2. apurinicapyrimidinic (AP) endonuclease excises the rest and creates a gap
3. DNA pol I and DNA ligase repair

Question 5

Nucleotide excision repair (4)

Answer 5

*Removal of pyrimidine dimers (thymine)

1. Repair system detects deformation in DNA helix
2. EvrABC endonuclease creates a nick to the left and right
3. UvrD helicase peels off DNA and leaves a gap
4. DNA pol I and DNA ligase repair

Prokaryotes: 7 proteins required

Eukaryotes: 25-29 proteins required; TFIIH involved

Question 6

Mismatch repair

Answer 6

1. MutS and MutL detect mismatch & scans for methyl grp on hemimethylated DNA shortly after replication, before deoxyadenosine methylase adds methyl grp to 2nd strnd *binding requires ATP MutL recruits other enzymes
2. MutH nicks newly synthesized strand at GATC *ATP MutH is only in bacteria
3. DNA helicase II unwinds DNA starting at nick and exonuclease creates gap up until mismatch
4. DNA pol III fills in

Question 7

Hereditary Nonpolyposis Colorectal Cancer

HNPCC

Answer 7

1. Mutant forms of hMLH1 and hMSH2 (mutL and mutS homologs)
2. cells proliferate continuously without correcting mismatch
3. Involved in development of inherited forms of colon cancer

also in endometrium, SI, stomach, upper urinary tract, ovary

Question 8

Xeroderma pigmentosum (XP)

Answer 8

Caused by mutation in TFIIH - NER fxn or in translesion DNA synthesis/error-prone DNA pol

1. Hypersensitivity to sun; UV thymine dimers cause cell apoptosis or tumor cells
2. High incidence of skin cancer
3. defective nucleotide excision repair; can’t fix thymine dimers. can’t introduce nicks
4. Obtain severe lesions, ulcerations, freckling with slight UV exposure

Question 9

Cockayne’s syndrome (CS)

&

Trichothiodystrophy

Answer 9

Problems in proper gene expression due to defects in transcription coupled repair of TFIIH, can’t recruit enzymes to resume txn

Growth retardation, neurological deficiencies, skeletal abnormalities, mild UV sensitivity

Brittle hair, short stature, scaly skin, mental retardation, mild UV sensitivity

When RNA encounters lesion, uncoupling factors allow RNA pol to back up from lesion so enzymes can come in to repair dimer. Then RNA pol continues without stalling and without aborting txn. key factor in promoting this process is TFIIH

Question 10

Homologous Recombination

Answer 10

1. Primary purpose in restarting DNA when a stall occurs
2. Secondary purpose in genetic diversity, reassortment of maternal and paternal alleles

*Role in meiosis: homologous chromatids align to form tetrades