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Flashcards in Genetics (Kurdistani) Deck (19):
1


Polymorphism


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

2

SNP vs. structural variant


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

3

Enhancer/Silencer


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

4


4 elements that core promoter can have

1) TFIIB recognition element

2) TATA box

3) INR initiator

4) Downstream core promoter element

5


CpG islands in core promoter


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)

6

Is RNAPolII enough to start transcription on its own?


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

7


Antibiotics/antifungals that inhibit transcription


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

8


Toxins that inhibit transcription

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

9

Antibiotics that inhibit translation

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

10


Epigenetics

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)

11


Nucleosome


DNA wrapped around a histone octamer which comprises a nucleosome

12


Histone deacetylases (HDAC)

Enzymes are mostly in transcription factor complexes

Deacetylation decreases DNA transcription

(Note: histone methylation decreases DNA transcription)

13


DNMT1


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

14


DNMT 3a and 3b


de novo methyltransferases that use unmethylated DNA as substrate

15


Are CG dinucleotides methylated in normal cells?


Yes, 70%

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

16


Methyl DNA binding proteins (MDBs)


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

17

Methyl guanine methyl transferase (MGMT or AGT)

(and its relevance to chemotherapy)

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.

18


Epigenetic drugs


DNMT inhibitor

HDAC inhibitor

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

 

19


miRNA


Primary --> Pre --> Single stranded with RISC

Complete match = mRNA degradation

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