Sandmeyer portion Flashcards
(34 cards)
What do topoisomerases do? What types are there and what is one example?
Topoisomerases are cellular enzymes that catalyze the removal or addition of supercoils. Type I cuts one strand of DNA and removes supercoils one link at a time; type II cuts two strands and removes two links at a time.
Gyrase is a Type II topoisomerase which removes positive supercoils.
Describe the most stable configuration for DNA.
Called B DNA. It is a right handed helix with 10.5 nts per turn, rotating the basis at 36 degrees.
What drug inhibits type II bacterial topoisomerases and bacterial gyrase?
Quinolones (e.g. nalidixic acid and ciprofloxacin). Novobiocin inhibits gyrase.
what does Novobiocin do?
aminocoumarin antibiotic which inhibits bacterial gyrase.
What are drugs used to treat cancer at the level of DNA synthesis?
- Daunorubicin and doxorubicin intercalate between the bases and interfere with topoisomerase activity
- Cisplatin interacts with N7 on guanine and crosslinks DNA; causes apoptosis
- Etoposide, a chemotherapy drug used to treat cancer patients, targets mammaliantopoisomerase II.
What is the temperature at which hybridization occurs most efficiently?
typically 5 deg C below the Tm temperature at which 50% of the molecules are denatured.
Which base pairs denature more readily than the other in DNA?
A - T denature more readily than G - C due to the the diff number of hydrogen bonds.
What factors affect the ability of polynucleotides to form duplexes?
- Salt
- pH
- Concentration
- Temperature.
- Complementary strand length
- Base composition
What kind of chromosomes do most bacteria have? What is the exception?
Most have one large circular chromosome. Borrelia, the causative agent of Lymes disease, has multiple circular and linear chromosomes.
What are the properties of a genome?
- Ability to replicate
- Ability to partition from mother to daughter cells
- Functional advantage
Where do prokaryotes concentrate the genome?
They concentrate the genome in the nucleoid which is not surrounded by a nuclear membrane.
How large is the genome for humans? number of genes?
3200 Mb. 21,000 genes. this discrepancy is due to the repetitive DNA common in eukaryotes especially humans.
Describe transcription.
Transcription is the process by which DNA is copied into RNA. It initiates with a 5’ nucleotide triphosphate.
Describe elongation.
sequential addition of nucleotide triphosphates at the 3’ OH with the generation of pyrophosphate and extension of the chain by one nucleotide.
Elongation requires locally unwinding the DNA ahead of the polymerase.
Which base pairs denature more readily than the other?
A-T base pairs denature more readily than G-C base pairs.
Factors affecting ability of polynucleotides to form duplexes?
Salt, pH, Concentration, Temperature, Complementary Strand Length, Base composition
What are critical parts of the promoter in prokaryotes?
-35, -10 regions and trasncription start site of +1.
What is the direction of building RNA in polymerization?
Proceeds building RNA from 5’ to 3’. It moves from 3’ to 5’ on the template strand.
Describe the two types of transcription termination in prokaryotes.
factor-independent: involves hair pin forming in RNA that destabilizes RNA pol. stretch of A’s in template DNA destabilizes the RNA pol.
factor-dependent term: there is a ttermiantion factor ρ (rho) which uses energy of ATP hydrolysis to unwind RNA: DNA duplexes. reduces stability of RNA:DNA heteroduplex behind polymerase and causes it to release.
What is the difference between DNA and RNA?
RNA
- has U instead of T.
- is more flexible.
- is typically single stranded
- 2’ -OH group alters structure and import in RNA processing
What are the types of mutations in ORFs ?
Silent which don’t change protein sequence. Missense which change the AA encoded. Nonsense if change to stop codon. Frame shift if change reading frame by multiples other than three.
What is deaminated form of the C base?
Uracil.
What are methods of mobilization of DNA within a cell
Expression cassettes which allow varied expression of surface antigens to evade immune system.
Transposable elements which can move among plasmids and genomes and are associated with bacterial populations.
What is bacterial transformation?
Integration by uptake of naked DNA by bacteria, by homologous recombination.
