Lecture 10: Genomic Regulation

Question 1

What do Nucleoside Analog Inhibitors do and what are examples of them?

Answer 1

• nucleosides lacking 3’-OH act as chain terminators that inhibit replication (convert to dNTPs first)

Ex:

• Ara-C –> leukemia
• AZT –> HIV therapy
• Acyclovir

Question 2

Ionizing Radiation damage types

Answer 2

• strand breaks, chemical base modification, DNA-protein cross-linking

Question 3

Non-ionizing Radiation damage types

Answer 3

• sunlight

- thymine dimers, thymine 6:4 covalent linkage

Question 4

Spontaneous Mutation damage types

Answer 4

1. Depurination –> lose 5000 purines/day
2. Deamination –> lose amine group
   • Cytosine –> Uracil
   • Adenine –> Hypoxanthine
   • Guanine –> Xanthine

Question 5

What are CpG islands?

Answer 5

• in promoter region; C-phosphate-G
• methylation coverts cytosine to thymine, causing stable silencing of genes (Cancer/DNA Repair genes)
• DNA repair relatively ineffective

Question 6

Cross-linking/Intercalation and carcinogens

Answer 6

• Benzo[a]pyrene converted to BPDE via colon enzymes

- converting procarcinogen into a carcinogen

Question 7

What are 4 common cross-linking agents?

Answer 7

1. nitrogen mustard (mustard gas)
2. cisplatin
3. mitomycin C
4. carmustine

Question 8

What are 2 common alkylating agents?

Answer 8

1. Dimethyl sulfate (DMS)

2. Methyl methanesulfonate (MMS)

Question 9

What is a common intercalating agent?

Answer 9

thalidomine

Question 10

MSH2/3/6, MLH1, PMS2 phenotype and defective enzyme

Answer 10

• colon cancer

- defective mismatch repair

Question 11

Xeroderma Pigmentosum phenotype and defective enzyme

Answer 11

• skin cancer, UV sensitivity, neurological abnormalities

- defective excision repair

Question 12

Ataxia telangiectasia phenotype and defective enzyme

Answer 12

• leukemia, lymphoma, genome instability

- defective ATM protein (protein kinase activated by DS breaks)

Question 13

BRCA2 phenotype and defective enzyme

Answer 13

• breast, ovarian, prostate cancer

- defective homologous recombination

Question 14

Fanconi Anemia phenotype and defective enzyme

Answer 14

• congenital abnormalities, leukemia, genome instability

- defective DNA interstrand cross-link repair

Question 15

Base Excision Repair

Answer 15

• repairs: single base mismatches, nondistorting alt.

- base, then backbone removed; polymerase repairs and ligase seals nick

Question 16

Nucleotide Excision Repair and diseases associated with its defect

Answer 16

• repair chemical adducts that distort DNA
• nicks DNA on both sides of damage site, removes DNA segment, then polymerase repairs
  diseases: Xeroderma Pigmentosum

Question 17

Mismatch Excision Repair and diseases associated with its defect

Answer 17

• MutS binds to mismatch, MutL scans for nick and removes nicked strand
  disease: Hereditary nonpolyposis colorectal cancer

Question 18

Double Stranded Break Repair (2 ways)

Answer 18

1. Nonhomologous End Joining (two flat ends stuck together) –> LOSE OF NUCLEOTIDES
2. Homologous End Joining (damage repaired using sister chromatid)

Question 19

Transcription-Coupled Repair and diseases associated with it

Answer 19

• DNA repair on sequences being actively transcribed by linking RNA polymerase with DNA repair
• RNA stalls at lesions and directs DNA repair machinery there
  disease: Cockaynes Syndrome

Question 20

Xeroderma Pigmentosum

Answer 20

• skin extremely sensitive to direct sunlight, prone to developing melanomas and squamous cell carcinoma
• UV light causes thymine dimer development
• proliferates in individuals w/defective NUCLEOTIDE EXCISION REPAIR (NER)

Question 21

Hereditary Nonpolyposis Colorectal Cancer

Answer 21

• defective in mismatch excision repair system (MER)

- loss of good copy of MER gene would allow tumor to grow

Question 22

Cockayne Syndrome

Answer 22

• defect in TRANSCRIPTION COUPLED REPAIR
• developmental/neurologic delay, photosensitivity, premature aging
• ERCC6/ERCC8 genes are mutated (autosomal recessive)

Question 23

BRCA Associated Breast Cancer

Answer 23

• mutations in BRCA1/2 tumor supressor genes

- defect in recombination repair system

Question 24

Histone Acetylation (HATs) and Histone Deacetylation (HDACs)

Answer 24

1. HATs - acetylate core histones to neutralize (+) charged Lysine = chromatin DECONDENSATION
   - HAT inhibitors show treatment of cancer, Alzheimers, rheumatoid arthritis
2. HDACs - remove acetyl groups from Lysines on core histones and nonhistone proteins
   - HDAC inhibitors valproic acid and vorinostate are used as anticonvulsive/anticancer drugs

Question 25

Rifampicin

Answer 25

• inhibits Bacterial RNA synthesis (antibiotic); binds to Beta subunit of RNA polymerase
• upregulates hepatic cytochrome P-450 and increases metabolism of other drugs
• red color to urine, sweat, and tears for short time after administration

Question 26

What are two common HDAC inhibitors?

Answer 26

vorinostat and entinostat

Question 27

Methylation

Answer 27

• methyl group added to cytosine and adenine
• represses gene transcription when at gene promoter
• happens at CpG Islands and helps stably silence genes

Question 28

Ubiquitin

Answer 28

• in eukaryotic cells; attaches to lysine 48/63 residues on target proteins
• Lysine 48 –> proteasome degradation
• Lysine 63 –> signaling, trafficking, endocytosis, DNA repair