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.
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.
The charge on histone octamer at pH 7 is +146. The charge on 150 bp DNA strand is -300.
Want to see more full solutions like this?
Chapter 33 Solutions
Biochemistry (Looseleaf)
- The glycolytic enzyme Phosphofructokinase (PFK) catalyzes the following reaction: Fructose-6-phosphate (F6P) + ATP → Fructose-1,6-bisphosphate (F1,6BP) + ADP AG"=-14.2 kJ/mol This is considered the enzymatic step that commits a sugar substrate to glycolysis. a) Calculate the standard free energy of hydrolysis of fructose-1,6-bisphosphate. b) What is the equilibrium constant for this coupled reaction? c) ATP is a known inhibitor of PFK. If the cellular concentrations of ATP and ADP are 5 mM and 1.0mM respectively, and the concentrations of F6P and F1,6BP are 2mM, what is the free energy change of the system?arrow_forward2) Consider the following reaction: A + 2B 3C + D At equilibrium the concentration of the reactants and products are: [A] = 20.0 mM [C] = 3.0 mM [B] = 4.0 mM [D] = 50.0 mM Calculate (a) the equilibrium constant and (b) AG". Comment on which side of this reaction is more likely to occur.arrow_forwardGlycine is a diprotic acid, which can potentially undergo two dissociation reactions, one for the a-amino group (NH), and the other for the carboxyl (-COOH) group. Therefore, it has two pK₁ values. The carboxyl group has a pK₁ of 2.34 and the α-amino group has a pK2 of 9.60. Glycine can exist in fully deprotonated (NH2-CH2-COO¯), fully protonated (NH3-CH2-COOH), or zwitterionic form (NH3-CH2-COO¯). Match the pH values with the corresponding form of glycine that would be present in the highest concentration in a solution of that pH. fully deprotonated form NH2-CH2-COO- fully protonated form NH–CH,–COOH zwitterionic form NH–CH,−COO Answer Bank pH 7.0 pH 11.9 pH 6.0 pH 8.0 pH 1.0arrow_forward
- The AG of hydrolysis of a sugar phosphate (S-O-P) to the free sugar (S-OH) is -26.6 kJ/mol in a hypothetical cell in which the steady-state concentrations of sugar phosphate, free sugar, and inorganic phosphate are 1.0 mM, 0.20 mM, and 50.0 mM, respectively. S-O-P + H2O S-OH + Pi (a) What is the AG°' for this reaction? (b) In the cell, S-O-P is formed by the transfer of a phosphate group from ATP. What would the AG be for the transfer of the g-phosphate from ATP to this sugar (S-OH)? [AG for ATP hydrolysis is -31 kJ/mol.]arrow_forward1) Consider the reaction: A B + C (a) What is the Keg for this reaction? AG= -8.80 kJ/mol (b) The reverse reaction is initiated by creating a solution containing 20mM B, 1mM A and 150mM C. At the instant these are mixed, what is the free energy change associated with the reaction?arrow_forwardWhat is the chemical importance of the negative charge on the phosphate group? Be asspecific as possible. In what ways might this negative charge have beenthermodynamically useful during the evolution of ATP-binding proteins?arrow_forward
- One prominent theory on life origins was that RNA enzymes came into existence early inthe prebiotic history of Earth and were able to do basic chemical catalyses. Eventually,this “RNA-world” was overtaken by the stability of DNA as an information carrier and thediversity of catalytic functions capable of being performed by polypeptides. Is the RNA world hypothesis is a well-founded model?arrow_forwardThe AG" of hydrolysis (ATP + H2O --> ADP + Pi) is -31.0 kJ/mol. Answer the following questions assuming that the steady-state concentrations in the cell are as indicated below. (Note: Steady-state refers to a non-equilibrium situation that exists due to a balance between reactions that supply and remove these substances.) [ADP] = 0.40 mM, [ATP] = 4.0 mM, and [Pi] = 40.0 mM a) Calculate the equilibrium constant for this reaction. b) What would the AG' for ATP hydrolysis be in the cell? c) Is this reaction at equilibrium in the cell? Briefly explain your answer.arrow_forward5) Theoretically, ATP did not have to become our bodies' main energy currency. Two alternative carriers, acetyl phosphate and S-adenosylmethionine could have been utilized, rather than ATP. AG" for acetyl phosphate hydrolysis is -43.3 kJ/mol and AG" for S- adenosylmethionine hydrolysis is -25.6 kJ/mol. (a) Calculate the weight of each alternative energy carrier that would need to be consumed by humans on a 2000 calorie per day diet if our bodies could not recycle it. Assume a 50% absorption of energy from our diet. (b) If our bodies contain 25g of each alternative energy carrier and they CAN be recycled, how many times would each molecule of each energy carrier need to be recycled? (c) Comment on the special properties of ATP and why it is unlikely that these alternative carriers would be utilized biologically.arrow_forward
- Give three reasons why evolution may have selected for phosphates compared to othersimilar leaving groups such as conjugated carboxylic acids or amides. Explain whatbenefit each of your reasons has granted to the living organism.arrow_forwardThe preferred substrate is T because the enzyme half-saturates at 7.00 mM for T, but requires 28.0 mM for U, and 112 mM for S. b Question Content Area The rate constant k 2 with substrate S is 9.60×107 sec-1, with substrate T, k 2 = 6.00×104 sec-1, and with substrate U, k 2 = 2.40×106 sec-1. Calculate the catalytic efficiency with S, T, and U. Catalytic efficiency with S = Catalytic efficiency with T = Catalytic efficiency with U = Does enzyme A use substrate S, substrate T, or substrate U with greater catalytic efficiency?arrow_forwardFumerase catalyzes the conversion of fumerate to malate. fumerate + H2O ⇋ malate The turnover number, kcat, for fumerase is 8.00×102 sec-1. The Km of this enzyme for fumerate is 5.00×10-3 μmol mL-1. a In an experiment using 2.00×10-3 μmol·mL-1, what is Vmax?arrow_forward
BiochemistryBiochemistryISBN:9781305577206Author:Reginald H. Garrett, Charles M. GrishamPublisher:Cengage Learning
Biology (MindTap Course List)BiologyISBN:9781337392938Author:Eldra Solomon, Charles Martin, Diana W. Martin, Linda R. BergPublisher:Cengage Learning
BiochemistryBiochemistryISBN:9781305961135Author:Mary K. Campbell, Shawn O. Farrell, Owen M. McDougalPublisher:Cengage Learning
Biology: The Unity and Diversity of Life (MindTap...BiologyISBN:9781305073951Author:Cecie Starr, Ralph Taggart, Christine Evers, Lisa StarrPublisher:Cengage Learning
Biology 2eBiologyISBN:9781947172517Author:Matthew Douglas, Jung Choi, Mary Ann ClarkPublisher:OpenStax