Genetics (Kurdistani)

Question 1

Polymorphism

Answer 1

Mutation that does not have an obvious effect on biology

Must be >1% prevalence in popultion

Arise because of founder effect or because they’re advantageous

Note: 90% of polymorphisms are SNPs

Question 2

SNP vs. structural variant

Answer 2

SNP: single nucleotide polymorphism (notes: two people have several million nucleotide differences! 2/3 in non-coding regions)

Structural variant: any variation that is not a SNP

Question 3

Enhancer/Silencer

Answer 3

DNA elements that stimulate (activator protein binds) or repress (repressor protein binds) transcription from a distance

Question 4

4 elements that core promoter can have

Answer 4

1) TFIIB recognition element
2) TATA box
3) INR initiator
4) Downstream core promoter element

Question 5

CpG islands in core promoter

Answer 5

Usually unmethylated, allowing transcription

In cancer, are methylated, turning off genes that could regulate cell cycle (Note: OTHER regions of DNA in cancer cells are hypo-methylated, leading to chromosomal instability)

Question 6

Is RNAPolII enough to start transcription on its own?

Answer 6

No, needs general transcription factors (GTFs) to form pre-initiation complex

Question 7

Antibiotics/antifungals that inhibit transcription

Answer 7

Rifampicin: antibiotic inhibits bacterial DNA-dependent RNA polymerase by locking promoter in “abortive initiation” reaction (used as anti-TB drug)

Flucytosine: antifungal that interferes with RNA and DNA synthesis in yeast

Question 8

Toxins that inhibit transcription

Answer 8

Diphtheria toxin (Pseudomonas toxin): ADP-ribosylates histidine in human EF-2 to block its activity

Ricin A chain: depurinates an adenine in 28S subunit of ribosomal RNA

Question 9

Antibiotics that inhibit translation

Answer 9

Streptomycin: antibiotic binds prokaryotic ribosomes and interferes with initiation

Tetracyclin: antibiotic binds ribosomes and interferes with AA-tRNA binding

Puromycin: resembles AA-tRNA and binds A site and causes premature termination

Question 10

Epigenetics

Answer 10

Heritable changes in gene expression mediated by mechanisms other than alterations in primary nucleotide sequence

These post-transcriptional modifications are reversible, modulated by enzymes

1) DNA methylation
2) Histone modification (methylation, acetylation, phospholylation, etc)
3) Regulatory non-coding RNAs (siRNA, miRNA, dsRNA, shRNA, transcripts from repeated sequences–ALU or LTR, ribosomal and transfer RNAs)

Question 11

Nucleosome

Answer 11

DNA wrapped around a histone octamer which comprises a nucleosome

Question 12

Histone deacetylases (HDAC)

Answer 12

Enzymes are mostly in transcription factor complexes

Deacetylation decreases DNA transcription

(Note: histone methylation decreases DNA transcription)

Question 13

DNMT1

Answer 13

DNA methyltransferase that replicates methylation of old strand on new strand after synthesis of new DNA

Question 14

DNMT 3a and 3b

Answer 14

de novo methyltransferases that use unmethylated DNA as substrate

Question 15

Are CG dinucleotides methylated in normal cells?

Answer 15

Yes, 70%

In cancer cells, DNA (non-promoter) is hypo-methylated which leads to chromosome instability

Question 16

Methyl DNA binding proteins (MDBs)

Answer 16

Repress transcription by recognizing methylated DNA sequences (in promoter?) and recruiting repressive protein complexes like HDACs

Question 17

Methyl guanine methyl transferase (MGMT or AGT)

(and its relevance to chemotherapy)

Answer 17

DNA repair enzyme

Removes methylation from guanine bases

Chemotherapeutic alkylating agents like temozolamide and carmustine kill cancer cells by causing damage to tumor DNA. However, test tumor cells for MGMT, because if they have it, they will respond less well to chemotherapy. We hope that cancer cells have silenced their MGMT gene by methylation so then they’re more susceptible to chemotherapy.

Question 18

Epigenetic drugs

Answer 18

DNMT inhibitor

HDAC inhibitor

(Cancer cells have tumor suppressor genes or DNA repair enzymes silenced via DNA methylation and histone deacetylation)

Question 19

miRNA

Answer 19

Primary –> Pre –> Single stranded with RISC

Complete match = mRNA degradation

Incomplete match = Translational inhibition or transcriptional inhibition (histone methylation)