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Chemistry 381: Introduction to Biological Chemistry
Homework Assignment # 2
Due: Fri. October 30, 2015 (by 5 pm)
1. Explain how, and state why the absorbance at 260 nm (A 260 ) can be used to determine if a
double helix forms from 2 single strands of DNA or RNA.
2.
(a) Define “base stacking”
(b) Describe the three predominant types of forces that contribute to stabilization of stacked
bases in a double helix.
3.
(a) What are counterions and why do they bind all nucleic acids?
(b) How do histones serve this function in the case of most chromosomal DNAs?
4. Give two reasons why G-C base pairs are more stable than A-T (or A-U) base pairs. Rank
these contributions according to importance in inducing stability.
Chemistry 381: Introduction to Biological Chemistry
Homework Assignment # 2
Due: Fri. October 30, 2015 (by 5 pm)
1. Explain how and why the absorbance at 260 nm (A 260 ) can be used to determine if a double
helix forms from 2 single strands of DNA or RNA.
Ans.
When two strands of DNA anneal to form a double helix, their absorbance at 260 nm decreases
relative to the sum of A 260 of the individual strands. This hypochromicity is used to determine
the extent of duplex formation.
2.
(a) Define “base stacking”
(b) Describe the three predominant types of forces that contribute to stabilization of stacked
bases in a double helix.
Ans.
(a) Bases “stack” on each other, face to face, like coins in a roll. Base-pair stacking is the
primary stabilizing force maintaining the double helical structure.
(b) Forces listed according to relative contributions to stabilization are:
1) The hydrophobic effect – in which water encages the bases at low T.
2) London dispersion forces – transient dipole-dipole attractions that involve the pi
electrons.
3) Hydrogen bond formation – which helps reinforce the stacked geometry.
3.
(a) What are counterions and why do they bind all nucleic acids?
(c) How do histones serve this function in the case of most chromosomal DNAs?
Ans.
(a) Nucleic acids have one electronegative phosphodiester phosphate, of which 0.1 unit of
negative charge is present per nucleotide. Ninety percent of the negative charge is
neutralized by the cation charges, which achieves near electroneutrality, and thereby
maintain thermodynamic stability.
(b) Histones are rich in the electropositive (basic) amino acid residues lysine and arginine.
These positive charges neutralize the negative charge of chromosomal DNA, which
allows the strands to become condensed and packaged within the chromosome.
4. Give two reasons why G-C base pairs are more stable than A-T (or A-U) base pairs. Rank
these contributions according to importance in inducing stability.
Ans.
The bases are ranked according to hydrophobicity as follows: G > A > C > T (or U), so G-C is
more hydrophobic than A-T (or A-U). the hydrophobic effect is the predominant stabilizing force
in base pairing. In addition, G-C base pairs have 3 hydrogen bonds while A-T (or A-U) only
have 2. Due to more extensive electronic overlap, London dispersion forces and stacking are also
more stabilizing for G-C versus A-T or A-U.