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JH. biochem exam 1 > Sandmeyer portion > Flashcards

Sandmeyer portion Flashcards

0
Q

What do topoisomerases do? What types are there and what is one example?

A

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.

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1
Q

Describe the most stable configuration for DNA.

A

Called B DNA. It is a right handed helix with 10.5 nts per turn, rotating the basis at 36 degrees.

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2
Q

What drug inhibits type II bacterial topoisomerases and bacterial gyrase?

A

Quinolones (e.g. nalidixic acid and ciprofloxacin). Novobiocin inhibits gyrase.

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3
Q

what does Novobiocin do?

A

aminocoumarin antibiotic which inhibits bacterial gyrase.

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4
Q

What are drugs used to treat cancer at the level of DNA synthesis?

A
  • 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.
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6
Q

What is the temperature at which hybridization occurs most efficiently?

A

typically 5 deg C below the Tm temperature at which 50% of the molecules are denatured.

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7
Q

Which base pairs denature more readily than the other in DNA?

A

A - T denature more readily than G - C due to the the diff number of hydrogen bonds.

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8
Q

What factors affect the ability of polynucleotides to form duplexes?

A
  1. Salt
  2. pH
  3. Concentration
  4. Temperature.
  5. Complementary strand length
  6. Base composition
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9
Q

What kind of chromosomes do most bacteria have? What is the exception?

A

Most have one large circular chromosome. Borrelia, the causative agent of Lymes disease, has multiple circular and linear chromosomes.

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10
Q

What are the properties of a genome?

A
  1. Ability to replicate
  2. Ability to partition from mother to daughter cells
  3. Functional advantage
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11
Q

Where do prokaryotes concentrate the genome?

A

They concentrate the genome in the nucleoid which is not surrounded by a nuclear membrane.

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12
Q

How large is the genome for humans? number of genes?

A

3200 Mb. 21,000 genes. this discrepancy is due to the repetitive DNA common in eukaryotes especially humans.

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13
Q

Describe transcription.

A

Transcription is the process by which DNA is copied into RNA. It initiates with a 5’ nucleotide triphosphate.

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14
Q

Describe elongation.

A

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.

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15
Q

Which base pairs denature more readily than the other?

A

A-T base pairs denature more readily than G-C base pairs.

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16
Q

Factors affecting ability of polynucleotides to form duplexes?

A 
Salt,
pH,
Concentration,
Temperature,  
Complementary Strand Length,
Base composition
17
Q

What are critical parts of the promoter in prokaryotes?

A

-35, -10 regions and trasncription start site of +1.

18
Q

What is the direction of building RNA in polymerization?

A

Proceeds building RNA from 5’ to 3’. It moves from 3’ to 5’ on the template strand.

19
Q

Describe the two types of transcription termination in prokaryotes.

A

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.

22
Q

What is the difference between DNA and RNA?

A

RNA

  • has U instead of T.
  • is more flexible.
  • is typically single stranded
  • 2’ -OH group alters structure and import in RNA processing
23
Q

What are the types of mutations in ORFs ?

A

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.

24
Q

What is deaminated form of the C base?

A

Uracil.

25
Q

What are methods of mobilization of DNA within a cell

A

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.

26
Q

What is bacterial transformation?

A

Integration by uptake of naked DNA by bacteria, by homologous recombination.

27
Q

What is conjugation in bacteria?

A

Some plasmids are self transmissible and encode a pilus which mediates contact with other bacteria. Allows cleavage and transfer of one strand of plasmid into recipient cell.

28
Q

What are the two different cycles that viruses and phages might undergo?

A

Lytic which involves release of many new phages upon lyse of cell wall. Lysogenic cycle integrates phage DNA as part of target genome,

29
Q

Transduction?

A

Ability of lysogenic phages to acquire bits of host genome and transfer to new host.

30
Q

How large is the human genome?

A

3.2 Gb.. With 22 somatic chrom and 2 sex chrom,

31
Q

What are retrotransposons?

A

Transposons that involve a RNA intermediate that is reverse transcripted into DNA . They include endogenous retroviruses, short interspersed elements SINES and LINES.

32
Q

In cytogenic analysis of metaphase chromosomes what is useful?

A

G- banding pattern when treated lightly with trypsin and Giesma stained. SINE areas are GC rich so lightly stained while LINE sequences are AT rich and thus darkly stained.

33
Q

What are alpha satellite DNA?

A

Thousands of copies of 171 BP repeats around centromeres.

34
Q

Nucleosomes repeat about every how many base pairs?

A

About 200 BP, since around 140 BP wrap around nucleosome and then each nucleosome is separate by about 69 BP.

35
Q

Histones are modified in what ways and how?

A

Methylation, acetylation of lysine , phosphorylation of serines.

By his tone methylases, demethylases, acetylases (HATs) , deacetylases (HDACs) , and kinases and phosphatases.

36
Q

Acetylation of histones does what?

A

Generally reduces positive charge on histone tails and thus makes them less tightly associated with negatively charged DNA.

JH. biochem exam 1 (3 decks)

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