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21 Cards in this Set
- Front
- Back
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TATA box binding protein is
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highly structurally conserved in most organisms (thermophiles, plants, humans)
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structural components of DNA
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nitrogenous base, deoxyribose sugar, phosphate
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how many h-bonds in guanine-cytosine? adenine-thymine?
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3 in G-C, 2 in A-T
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C-C and C=O (how long and what is bond energy?)
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C-C= 1.54A and 85kcal/mol
C=O=1.34A and 175kcal/mol |
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Coulomb's Law equation
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E=kq1q2/Dr^2
E=energy q1 and q2=charges on 2 atoms r=distance btw 2 atoms D=dielectric constant k=proportionality constant |
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the dielectric constant accounts for...
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the effects of intervening medium
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H-bond donor; H-bond receiver
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donor=group containing H convalently linked to other molecule
receiver=group containing H weakly linked to other molecule |
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dielectric constant of water
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80
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typical range of energy for van der Waals interactions
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0.5-1.0 kcal/mole
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van der Waals contact distance
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when molecules grow closer than this distance, strong repulsive forces become dominant with overlap of electron clouds
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typical range of energy for H-bonds
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1-5 kcal/mol
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distance from H to N in H-bond
distance from H to O in H-bond |
H---N=1.5-2.6A
H---O=2.4-3.3A |
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dielectric constant for hexane is greater or less than for water
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less (2 vs 80); results in E being much higher
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water weakens electrostatic and H-bonds by
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competing
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hydrophobic effect
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water surround nonpolar molecules in ordered fashion; when nonpolar molecules coalesce, water is released resulting in more disorder of water (increased entropy)
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DNA bases are (hydrophobic or hydrophilic)
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hydrophobic so stacked inside
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1st and 2nd law of thermodynamics
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1) energy can't be created or destroyed
2) total entropy of a system is always increasing for spontaneous processes |
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deltaG=
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deltaH(of system)-TdeltaS(of system)<0
delta H=heat of system delta S=entropy of system |
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Henderson-Hasselbach Equation
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pH=pKa+log([A-]/[HA]); when pH=pKa, [A]=[HA]
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the max buffering of acetate is at its...;when all acetate has been converted to acetic acid...
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pKa; pH drops quickly
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an example of a natural buffer; which forms are biologically relevant?
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phosphate (H3PO4); monobasic and dibasic forms are biologically relevant (H2PO4 and HPO4)
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