Chapter 33, Problem 1P

Interpretation Introduction

Interpretation:

The charge on histone octamer at pH 7 should be determined.

The charge on the histone should be compared with a charge on 150 bp DNA.

Concept introduction:

There are around 300 amino acids, but only 22 amino acids participate in protein synthesis. Such amino acids are termed as proteinogenic amino acids. Some amino acids are very common in protein chain, while some amino acids are rare in protein chain. The most abundant amino acids in the protein chain are leucine, serine, lysine, and glutamic acid.

Answer to Problem 1P

The charge on histone octamer at pH 7 is +146. The charge on 150 bp DNA strand is -300.

Explanation of Solution

Given information:

The histone octamer is at pH 7, and histidine neutralizes at this pH.

Histone H2A protein chain-

In histone H2A protein sequence, there are 4 charged amino acids, lysine, arginine, aspartic acid, and glutamic acid. Lysine amino acid has -NH₃+ as the side chain, which ionizes at pH of 10.54. Therefore, at pH 7, this side chain of lysine will not neutralize, giving lysine residue +1 charge. There are 13 lysine residues, hence, charge on protein due to lysine is +13.

Arginine amino acid also has -NH₃+ as the side chain, which ionizes at pH of 12.48. Therefore, at pH 7, this side chain of arginine will not neutralize, giving arginine residue +1 charge. There are 13 arginine residues, hence, charge on protein due to arginine is +13.

Aspartic acid has -COO- as side chain. This side chain ionizes when pH of the solution reaches to 3.86. At pH 7, -COO- will not accept the hydrogen ion, hence, the charge of aspartic acid will be -1. There are total 2 aspartate amino acids, therefore, the charge on protein due to this amino acid is -2.

Glutamic acid has -COO- as side chain. This side chain ionizes when pH of the solution reaches to 4.25. At pH 7, -COO- will not accept the hydrogen ion, hence, the charge of glutamic acid will be -1. There are total 7glutamate amino acids, therefore, the charge on protein due to this amino acid is -7.

Hence, total charge on H2A protein sequence = +13+13+ (-2) +(-7) = +17.

Histone H2B protein chain-

In histone H2B protein sequence, there are 4 charged amino acids, lysine, arginine, aspartic acid, and glutamic acid. Lysine amino acid has -NH₃+ as the side chain, which ionizes at pH of 10.54. Therefore, at pH 7, this side chain of lysine will not neutralize, giving lysine residue +1 charge. There are 20 lysine residues, hence, charge on protein due to lysine is +20.

Arginine amino acid also has -NH₃+ as the side chain, which ionizes at pH of 12.48. Therefore, at pH 7, this side chain of arginine will not neutralize, giving arginine residue +1 charge. There are 8 arginine residues, hence, charge on protein due to arginine is +8.

Aspartic acid has -COO- as side chain. This side chain ionizes when pH of the solution reaches to 3.86. At pH 7, -COO- will not accept the hydrogen ion, hence, the charge of aspartic acid will be -1. There are total 3 aspartate amino acids, therefore, the charge on protein due to this amino acid is -3.

Glutamic acid has -COO- as side chain. This side chain ionizes when pH of the solution reaches to 4.25. At pH 7, -COO- will not accept the hydrogen ion, hence, the charge of glutamic acid will be -1. There are total 7 glutamate amino acids, therefore, the charge on protein due to this amino acid is -7.

Hence, total charge on H2A protein sequence = +20+8+ (-3) +(-7) = +18.

Histone H3B protein chain-

In histone H3B protein sequence, there are 4 charged amino acids, lysine, arginine, aspartic acid, and glutamic acid. Lysine amino acid has -NH₃+ as the side chain, which ionizes at pH of 10.54. Therefore, at pH 7, this side chain of lysine will not neutralize, giving lysine residue +1 charge. There are 13 lysine residues, hence, charge on protein due to lysine is +13.

Arginine amino acid also has -NH₃+ as the side chain, which ionizes at pH of 12.48. Therefore, at pH 7, this side chain of arginine will not neutralize, giving arginine residue +1 charge. There are 18 arginine residues, hence, charge on protein due to arginine is +18.

Aspartic acid has -COO- as side chain. This side chain ionizes when pH of the solution reaches to 3.86. At pH 7, -COO- will not accept the hydrogen ion, hence, the charge of aspartic acid will be -1. There are total 4 aspartate amino acids, therefore, the charge on protein due to this amino acid is -4.

Glutamic acid has -COO- as side chain. This side chain ionizes when pH of the solution reaches to 4.25. At pH 7, -COO- will not accept the hydrogen ion, hence, the charge of glutamic acid will be -1. There are total 7 glutamate amino acids, therefore, the charge on protein due to this amino acid is -7.

Hence, total charge on H3A protein sequence = +13+18+ (-4) +(-7) = +20.

Histone H4B protein chain-

In histone H4B protein sequence, there are 4 charged amino acids, lysine, arginine, aspartic acid, and glutamic acid. Lysine amino acid has -NH₃+ as the side chain, which ionizes at pH of 10.54. Therefore, at pH 7, this side chain of lysine will not neutralize, giving lysine residue +1 charge. There are 11 lysine residues, hence, charge on protein due to lysine is +11.

Arginine amino acid also has -NH₃+ as the side chain, which ionizes at pH of 12.48. Therefore, at pH 7, this side chain of arginine will not neutralize, giving arginine residue +1 charge. There are 14 arginine residues, hence, charge on protein due to arginine is +14.

Aspartic acid has -COO- as side chain. This side chain ionizes when pH of the solution reaches to 3.86. At pH 7, -COO- will not accept the hydrogen ion, hence, the charge of aspartic acid will be -1. There are total 3 aspartate amino acids, therefore, the charge on protein due to this amino acid is -3.

Glutamic acid has -COO- as side chain. This side chain ionizes when pH of the solution reaches to 4.25. At pH 7, -COO- will not accept the hydrogen ion, hence, the charge of glutamic acid will be -1. There are total 4 glutamate amino acids, therefore, the charge on protein due to this amino acid is -4.

Hence, total charge on H4A protein sequence = +11+14+ (-3) +(-4) = +18.

$\begin{array}{l}Totalchargeonhistonetetramer=17+18+20+18=+73\hfill \\ Therefore,chargeonhistoneoctamer=2\times 73=+146\hfill \end{array}$

There is a DNA with 150 bp.This means total number of bases in DNA strand are 300. Each base has -1 charge on it due to the presence of phosphate group. So, the total charge on DNA strand is -300. So, if this DNA strand binds around the above histone octamer, then half of the charges on DNA would get neutralized.

Conclusion

The charge on histone octamer at pH 7 is +146. The charge on 150 bp DNA strand is -300.