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22 Cards in this Set
- Front
- Back
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General structure of DNA |
Right handed, B form helix Grooves for proteins (major and minor), repeats every 36 angstroms or 10.5 residues |
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Phophodiester bond |
Connects phosphate 3' to 5' carbons of deoxyribose |
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Actinomycin: |
antibiotic, anticancer drug that interacts with grooves of DNA to stop enzymes in replication/transcription |
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Hydrogen bonds |
Connect two strands; bases stacked perpendicular to share electrons, stabilize structure |
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Two other DNA structures |
A form: compact (28 angstrom) in vivo
Z form: alternating purines/pyrimidines, may have role in gene expression |
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Denaturing of DNA |
Can be caused by --changes in pH --changes in ionic concentration of solution --heating |
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FISH |
technique that uses flourescent pieces of complementary DNA
by denaturing your DNA in question, you can see if cDNA binds to it
Way to determine chromosome rearrangement |
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Denatured DNA, spectroscopy |
260 nm wavelength causes a jump in absorbance because bases now open to absorb light |
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Melting Temperature of DNA |
Tm, when 50% of DNA is denatured
Higher Tm of DNA with more GC bonds (3 hydrogen bonds versus 2)
More ionic solution leads to an increase in Tm |
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Supercoiling |
When torsional stress (potential energy) increases, causes DNA to wind; when it winds/twists more than average, we get this |
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Circular DNA and supercoiling |
Can be relaxed (to 10.5 bp per turn)
Positive supercoil=twisting tigheter Negative supercoil=unwinding DNA, for replication/transcription |
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Huge linear chromosomes and supercoiling |
Behave just like circular DNA, basically tied at ends |
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Topisomerases |
Enzymes that relive stress for supercoiling
Two types: type 1 and type 2 |
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Type 1 topisomerases |
Cleaves 1 strand DNA, passes strand thru, then reseals
Energy independent
Relieves 1 turn
Relax positive and negative supercoils |
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Type 2 topisomerases |
Cleaves 2 DNA strands, passes both thru the break and then reseals
Energy dependent
Relieves 1 turn
Relax positive and negative supercoils |
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Steps of Type 1 Topisomerase |
1. Tyr attachs phosphodiester bond, binding to it (nucleophilic attack)
2. Enzyme opens, brings other unbroken strand through
3. OH from broken strand attacks phosphate, binds to it cleaving of enzyme |
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Steps of Type 2 Topisomerase |
1. Enzyme binds DNA, second segment of DNA at N gate
2. Original DNA cleaved, second segment passed thru
3. DNA resealed, released via C gate |
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Coumarins |
antibiotic that inhibits type II topoisomerases from binding ATP so transcription cannot occur
example: novobiocin, coumermycin A1 |
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Quinolones |
inhibit resealing breaks of topisomerases so supercoiling cannot be relieved and transcription cannot occur
most selective
example: naliolixic acid, ciproflacxacin, Cipro |
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Chemotherapy agents and topoisomerases |
Tumors express too much type II topisomerases, so chemotherapy agents inhibit this
However, more likely to damage good DNA through inhibiting these topisomerases, which is why hair falls out/your body shuts down from chemo |
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Eukaryotic topoisomeraes type 1 inhibitors |
Trap DNA complex in cleaved state
Example: captothecin, irinolecar, topotecan |
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Eukaryotic topoisomerases type 2 inhibitors |
Example: Doxoruloicin, etoposide, elleptiuine |
