1 Chapter The Foundations of Biochemistry
Multiple Choice Questions
1. Chemical foundations Page: 14 Difficulty: 1 Ans: B What functional groups are present on this molecule?
A) ether and aldehyde B) hydroxyl and aldehyde C) hydroxyl and carboxylic acid D) hydroxyl and ester E) hydroxyl and ketone 2. Chemical foundations Page: 17 Difficulty: 1 Ans: D Stereoisomers that are nonsuperimposable mirror images of each other are known as: A) anomers. B) cis-trans isomers. C) diastereoisomers. D) enantiomers. E) geometric isomers. 3. Physical foundations Page: 23 Difficulty: 1 Ans: C If heat energy is absorbed by the system during a chemical reaction, the reaction is said to be: A) at equilibrium. B) endergonic. C) endothermic. D) exergonic. E) exothermic. 4. Physical foundations Page: 23 Difficulty: 2 Ans: D If the free energy change G for a reaction is -46.11 kJ/mol, the reaction is: A) at equilibrium. B) endergonic. C) endothermic. D) exergonic. E) exothermic. 5. Physical foundations Page: 26 Difficulty: 2
Ans: A
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Chapter 1 The Foundations of Biochemistry
Enzymes are biological catalysts that enhance the rate of a reaction by: decreasing the activation energy. B) decreasing the amount of free energy released. C) increasing the activation energy. D) increasing the amount of free energy released. E) increasing the energy of the transition state. 6. Physical foundations Page: 27 Difficulty: 1 Ans: B Energy requiring metabolic pathways that yield complex molecules from simpler precursors are:
A)
A) amphibolic. B) anabolic. C) autotrophic. D) catabolic. E) heterotrophic. 7. Genetic foundations Page: 30 Difficulty: 2 Ans: E The three-dimensional structure of a protein is determined primarily by: A) B) C) D) E) electrostatic guidance from nucleic acid structure. how many amino acids are in the protein. hydrophobic interaction with lipids that provide a folding framework. modification during interactions with ribosomes. the sequence of amino acids in the protein.
Short Answer Questions
8. Cellular foundations Page: 11 Difficulty: 2 (a) List the types of noncovalent interactions that are important in providing stability to the threedimensional structures of macromolecules. (b) Why is it important that these interactions be noncovalent, rather than covalent, bonds? Ans: (a) Noncovalent interactions include hydrogen bonds, ionic interactions between charged groups, van der Waals interactions, and hydrophobic interactions. (b) Because noncovalent interactions are weak, they can form, break, and re-form more rapidly and with less energy input than can covalent bonds. This is important to maintain the flexibility needed in macromolecules. 9. Chemical Foundations Pages: 17-18 Difficulty: 2 Why is an asymmetric carbon atom called a chiral center? Ans: An asymmetric carbon has four different substituents attached, and cannot be superimposed on its mirror imageas a right hand cannot fit into a left glove. Thus a molecule with one chiral carbon will have two stereoisomers, which may be distinguishable from one another in a biological system. 10. Chemical foundations Pages: 17, 20 Difficulty: 3 Differentiate between configuration and conformation. Ans: Configuration denotes the spatial arrangement of the atoms of a molecule that is conferred by
Chapter 1 The Foundations of Biochemistry
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the presence of either double bonds, around which there is no freedom of rotation, or chiral centers, which give rise to stereoisomers. Configurational isomers can only be interconverted by temporarily breaking covalent bonds. Conformation refers to the spatial arrangement of substituent groups that, without breaking any bonds, are free to assume different positions in space because of the freedom of bond rotation. 11. Chemical foundations Pages: 17, 19 Difficulty: 3 (a) What is optical activity? (b) How did Louis Pasteur arrive at an explanation for the phenomenon of optical activity? Ans: (a) Optical activity is the capacity of a substance to rotate the plane of plane-polarized light. (b) Using fine forceps, he was able to separate the two types of crystals found in tartaric acid (racemic acid) that are identical in shape, but mirror images of each other. One sample rotated polarized light to the left; the mirror image crystals rotated polarized light to the right. 12. Chemical foundations Pages: 20-21 Difficulty: 3 A chemist working in a pharmaceutical lab synthesized a new drug as a racemic mixture. Why is it important that she separate the two enantiomers and test each for its biological activity? Ans: Biomolecules such as receptors for drugs are stereospecific, so each of the two enantiomers of the drug may have very different effects on an organism. One may be beneficial, the other toxic; or one enantiomer may be ineffective and its presence could reduce the efficacy of the other enantiomer. 13. Physical foundations Page: 23 Difficulty: 2 The free-energy change for the formation of a protein from the individual amino acids is positive and is thus an endergonic reaction. How, then, do cells accomplish this process? Ans: The endergonic (thermodynamically unfavorable) reaction is coupled to an exergonic (thermodynamically favorable) reaction through a shared intermediate, so that the overall free-energy change of the coupled reactions is negative (the overall reaction is exergonic). 14. Physical foundations Pages: 26-27 Difficulty: 2 (a) On the reaction coordinate diagram shown below, label the transition state and the overall freeenergy change ( G) for the uncatalyzed reaction A B. (b) Is this an exergonic or endergonic reaction? (c) Draw a second curve showing the energetics of the reaction if it were enzymecatalyzed.
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Chapter 1 The Foundations of Biochemistry
Ans: (a) and (c) (See Fig. 1-27, p. 27.) (b) exergonic reaction
Chapter 2 Water
Multiple Choice Questions
1. Weak interactions in aqueous systems Page: 4749 Difficulty: 2 Ans: D Which of these statements about hydrogen bonds is not true? A) Hydrogen bonds account for the anomalously high boiling point of water. B) In liquid water, the average water molecule forms hydrogen bonds with three to four other water molecules. C) Individual hydrogen bonds are much weaker than covalent bonds. D) Individual hydrogen bonds in liquid water exist for many seconds and sometimes for minutes. E) The strength of a hydrogen bond depends on the linearity of the three atoms involved in the bond. 2. Weak interactions in aqueous systems Page: 53 Difficulty: 2 Ans: A A true statement about hydrophobic interactions is that they: A) are the driving force in the formation of micelles of amphipathic compounds in water. B) do not contribute to the structure of water-soluble proteins. C) have bonding energies of approximately 2040 Kjoule per mole. D) involve the ability of water to denature proteins. E) primarily involve the effect of polar solutes on the entropy of aqueous systems. 3. Weak interactions in aqueous systems Page: 5354 Difficulty: 2 Ans: E Hydrophobic interactions make important energetic contributions to: A) binding of a hormone to its receptor protein. B) enzyme-substrate interactions. C) membrane structure. D) three-dimensional folding of a polypeptide chain. E) all of the above are true. 4. Ionization of water, weak acids, and weak bases Page: 60 Difficulty: 2 Ans: E A hydronium ion: A) has the structure H3O+. B) is a hydrated hydrogen ion. C) is a hydrated proton. D) is the usual form of one of the dissociation products of water in solution. E) all of the above are true. 5. Ionization of water, weak acids, and weak bases Page: 61 Difficulty: 2 Ans: A The pH of a solution of 1 M HCl is:
Chapter 1 The Foundations of Biochemistry
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A) 0 B) 0.1 C) 1 D) 10 E) 1 6. Ionization of water, weak acids, and weak bases Page: 62 Difficulty: 2 Ans: D Which of the following is true about the properties of aqueous solutions? A) A pH change from 5.0 to 6.0 reflects an increase in the hydroxide ion concentration ([OH-]) of 20%. B) A pH change from 8.0 to 6.0 reflects a decrease in the proton concentration ([H+]) by a factor of 100. C) Charged molecules are generally insoluble in water. D) Hydrogen bonds form readily in aqueous solutions. E) The pH can be calculated by adding 7 to the value of the pOH. 7. Ionization of water, weak acids, and weak bases Page: 62 Difficulty: 2 Ans: E The pH of a sample of blood is 7.4, while gastric juice is pH 1.4. The blood sample has: A) 0.189 times the [H+] as the gastric juice. B) 5.29 times lower [H+] than the gastric juice. C) 6 times lower [H+] than the gastric juice. D) 6,000 times lower [H+] than the gastric juice. E) a million times lower [H+] than the gastric juice. 8. Ionization of water, weak acids, and weak bases Page: 63 Difficulty: 1 Ans: D The aqueous solution with the lowest pH is: A) 0.01 M HCl. B) 0.1 M acetic acid (pKa = 4.86). C) 0.1 M formic acid (pKa = 3.75). D) 0.1 M HCl. E) 1012 M NaOH. 9. Ionization of water, weak acids, and weak bases Page: 63 Difficulty: 2 Ans: B Phosphoric acid is tribasic, with pKas of 2.14, 6.86, and 12.4. The ionic form that predominates at pH 3.2 is: A) H3PO4. B) H2PO4. C) HPO42. D) PO43. E) none of the above. 10. Buffering against pH changes in biological systems
Page: 6566
A) B)
Difficulty: 2 Ans: E
Which of the following statements about buffers is true? A buffer composed of a weak acid of pKa = 5 is stronger at pH 4 than at pH 6. At pH values lower than the pKa, the salt concentration is higher than that of the acid.
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Chapter 1 The Foundations of Biochemistry
C) The pH of a buffered solution remains constant no matter how much acid or base is added to the solution. D) The strongest buffers are those composed of strong acids and strong bases. E) When pH = pKa, the weak acid and salt concentrations in a buffer are equal. 11. Buffering against pH changes in biological systems Page: 6567 Difficulty: 3 Ans: D A compound has a pKa of 7.4. To 100 mL of a 1.0 M solution of this compound at pH 8.0 is added 30 mL of 1.0 M hydrochloric acid. The resulting solution is pH: A) 6.5 B) 6.8 C) 7.2 D) 7.4 E) 7.5 12. Buffering against pH changes in biological systems Page: 66-67 Difficulty: 2 Ans: E The Henderson-Hasselbalch equation: A) allows the graphic determination of the molecular weight of a weak acid from its pH alone. B) does not explain the behavior of di- or tri-basic weak acids C) employs the same value for pKa for all weak acids. D) is equally useful with solutions of acetic acid and of hydrochloric acid. E) relates the pH of a solution to the pKa and the concentrations of acid and conjugate base. 13. Buffering against pH changes in biological systems Page: 6667 Difficulty: 2 Ans: D Consider an acetate buffer, initially at the same pH as its pKa (4.76). When sodium hydroxide (NaOH) is mixed with this buffer, the: A) pH remains constant. B) pH rises more than if an equal amount of NaOH is added to an acetate buffer initially at pH 6.76. C) pH rises more than if an equal amount of NaOH is added to unbuffered water at pH 4.76. D) ratio of acetic acid to sodium acetate in the buffer falls. E) sodium acetate formed precipitates because it is less soluble than acetic acid. 14. Buffering against pH changes in biological systems Page: 6667 Difficulty: 2 Ans: C Three buffers are made by combining a 1 M solution of acetic acid with a 1 M solution of sodium acetate in the ratios shown below. 1 M acetic acid 1 M sodium acetate Buffer 1: 10 mL 90 mL Buffer 2: 50 mL 50 mL Buffer 3: 90 mL 10 mL Which of these statements is true of the resulting buffers? A) B) C) D) pH of buffer 1 < pH of buffer 2 < pH of buffer 3 pH of buffer 1 = pH of buffer 2 = pH of buffer 3 pH of buffer 1 > pH of buffer 2 > pH of buffer 3 The problem cannot be solved without knowing the value of pKa.
Chapter 1 The Foundations of Biochemistry
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E)
None of the above.
Short Answer Questions
15. Weak interactions in aqueous systems Page: 4755 Difficulty: 2 Name and briefly define four types of noncovalent interactions that occur between biological molecules. Ans: (1) Hydrogen bonds: weak electrostatic attractions between one electronegative atom (such as oxygen or nitrogen) and a hydrogen atom covalently linked to a second electronegative atom; (2) electrostatic interactions: relatively weak charge-charge interactions (attractions of opposite charges, repulsions of like charges) two between ionized groups; (3) hydrophobic interactions: the forces that tend to bring two hydrophobic groups together, reducing the total area of the two groups that is exposed to surrounding molecules of the polar solvent (water); (4) van der Waals interactions: weak interactions between the electric dipoles that two close-spaced atoms induce in each other. 16. Ionization of water, weak acids, and weak bases Page: 63 Difficulty: 1 For each of the pairs below, circle the conjugate base. RCOOH RNH2 H2PO4 H2CO3 RCOO RNH3+ H3PO4 HCO3
Ans: RCOO, RNH2, H2PO4, HCO3 17. Ionization of water, weak acids, and weak bases Page: 63 Difficulty: 2 Phosphoric acid (H3PO4) has three dissociable protons, with the pKas shown below. Which form of phosphoric acid predominates in a solution at pH 4? Explain your answer. Acid pKa H3PO4 2.14 H2PO4 HPO42 6.86 12.4
Ans: At pH 4, the first dissociable proton (pKa = 2.14) has been titrated completely, and the second (pKa = 6.86) has just started to be titrated. The dominant form at pH 4 is therefore H2PO4, the form with one dissociated proton (see Fig. 2-16). 18. Buffering against pH changes in biological systems Page: 6466 Difficulty: 2 Give the general Henderson-Hasselbalch equation and sketch the plot it describes (pH against amount of NaOH added to a weak acid). On your curve label the pKa for the weak acid, and indicate the region in which the buffering capacity of the system is greatest. Ans: The inflection point, which occurs when the weak acid has been exactly one half titrated with NaOH, occurs at a pH equal to the pKa of the weak acid. The region of greatest buffering capacity
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Chapter 1 The Foundations of Biochemistry
(where the titration curve is flattest) occurs at pH values of pKa 1. (See Fig. 2-18, p. 65.) 19. Buffering against pH changes in biological systems Page: 65 Difficulty: 3 Draw the titration curve for a weak acid, HA, whose pKa is 3.2. Label the axes properly. Indicate with an arrow where on the curve the ratio of salt (A) to acid (HA) is 3:1. What is the pH at this point? Ans: The plot of pH vs. added base should have the general shape of those shown in Fig. 2-18, p. 65, with the midpoint of the titration (inflection point) at pH 3.2. The ratio of A to HA is 3 when 0.75 equivalents of base have been added. From the Henderson-Hasselbalch equation, the pH at this point can be calculated: pH = pKa + log
[ o j gt c nu ae [ cd ai ] bs ] ae
= 3.2 + log 3 = 3.2 + 0.48 = 3.68
20. Buffering against pH changes in biological systems Page: 6667 Difficulty: 2 What is the pH of a solution containing 0.2 M acetic acid (pKa = 4.7) and 0.1 M sodium acetate? Ans: pH = pKa + log
[ o j gt c nu ae [ cd ai ] bs ] ae
= 4.7 + log (0.1/0.2)
= 4.7 0.3 = 4.4 21. Buffering against pH changes in biological systems Page: 6667 Difficulty: 2 You have just made a solution by combining 50 mL of a 0.1 M sodium acetate solution with 150 mL of 1 M acetic acid (pKa = 4.7). What is the pH of the resulting solution? Ans: pH = pKa + log
[ o j gt c nu ae [ cd ai ] bs ] ae
= 4.7 + log (5/150)
= 4.7 1.48 = 3.22 22. Buffering against pH changes in biological systems Page: 6667 Difficulty: 2 For a weak acid with a pKa of 6.0, show how you would calculate the ratio of acid to salt at pH 5. Ans:
23. Buffering against pH changes in biological systems Page: 66-67 Difficulty: 3 Suppose you have just added 100 mL of a solution containing 0.5 mol of acetic acid per liter to 400 mL of 0.5 M NaOH. What is the final pH? (The pKa of acetic acid is 4.7.) Ans: Addition of 200 mmol of NaOH (400 mL 0.5 M) to 50 mmol of acetic acid (100 mL 0.5 mM) completely titrates the acid so that it can no longer act as a buffer and leaves 150 mmol of
Chapter 1 The Foundations of Biochemistry
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NaOH dissolved in 500 mL, an [OH] of 0.3 M. Given [OH], [H+] can be calculated from the water constant: [H+][OH] = 1014 [H+] = 1014 M2 / 0.3 M pH is, by definition, log (1/[H+]) pH = log (0.3 M /1014 M2) = 12.48. 24. Buffering against pH changes in biological systems Page: 66-67 Difficulty: 2 A weak acid HA, has a pKa of 5.0. If 1.0 mol of this acid and 0.1 mol of NaOH were dissolved in one liter of water, what would the final pH be? Ans: Combining 1 mol of weak acid with 0.1 mol of NaOH yields 0.9 mol of weak acid and 0.1 mol of salt. pH = pKa + log
[ o j gt c nu ae [ cd ai ] bs ] ae
= 5.0 + log (0.1/0.9) = 4.05
Chapter 3 Amino Acids, Peptides, and Proteins
Multiple Choice Questions
1. Amino acids Page: 76 Difficulty: 1 Ans: C The chirality of an amino acid results from the fact that its carbon: has no net charge. is a carboxylic acid. C) is bonded to four different chemical groups. D) is in the L absolute configuration in naturally occurring proteins. E) is symmetric. 2. Amino acids Page: 76 Difficulty: 2 Ans: B Of the 20 standard amino acids, only ___________ is not optically active. The reason is that its side chain ___________. A) alanine; is a simple methyl group B) glycine; is a hydrogen atom C) glycine; is unbranched D) lysine; contains only nitrogen E) proline; forms a covalent bond with the amino group 3. Amino acids Page: 79 Difficulty: 1 Ans: A All of the amino acids that are found in proteins, except for proline, contain a(n): A) amino group. B) carbonyl group. A) B)
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Chapter 1 The Foundations of Biochemistry
C) carboxyl group. D) ester group. E) thiol group. 4. Amino acids Pages: 7980 Difficulty: 3 Ans: C Which of the following statements about aromatic amino acids is correct? A) All are strongly hydrophilic. B) Histidines ring structure results in its being categorized as aromatic or basic, depending on pH. C) On a molar basis, tryptophan absorbs more ultraviolet light than tyrosine. D) The major contribution to the characteristic absorption of light at 280 nm by proteins is the phenylalanine R group. E) The presence of a ring structure in its R group determines whether or not an amino acid is aromatic. 5. Amino acids Page: 80 Difficulty: 2 Ans: A Which of the following statements about cystine is correct? Cystine forms when the CH2SH R group is oxidized to form a CH2SSCH2 disulfide bridge between two cysteines. B) Cystine is an example of a nonstandard amino acid, derived by linking two standard amino acids. C) Cystine is formed by the oxidation of the carboxylic acid group on cysteine. D) Cystine is formed through a peptide linkage between two cysteines. E) Two cystines are released when a CH2SSCH2 disulfide bridge is reduced to CH2SH. 6. Amino acids Page: 81 Difficulty: 1 Ans: A Amino acids are ampholytes because they can function as either a(n):
A)
A) acid or a base. B) neutral molecule or an ion. C) polar or a nonpolar molecule. D) standard or a nonstandard monomer in proteins. E) transparent or a light-absorbing compound. 7. Amino acids Pages: 8283 Difficulty: 2 Ans: D Titration of valine by a strong base, for example NaOH, reveals two pKs. The titration reaction occurring at pK2 (pK2 = 9.62) is: A) COOH + OH COO + H2O. B) COOH + NH2 COO + NH2+. C) COO + NH2+ COOH + NH2. + D) NH3 + OH NH2 + H2O. E) NH2 + OH NH + H2O. 8. Amino acids Page: 84 Difficulty: 2 Ans: B For amino acids with neutral R groups, at any pH below the pI of the amino acid, the population of amino acids in solution will have:
Chapter 1 The Foundations of Biochemistry
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A) a net negative charge. B) a net positive charge. C) no charged groups. D) no net charge. E) positive and negative charges in equal concentration. 9. Peptides and proteins Page: 86 Difficulty: 1 Ans: C The peptide alanylglutamylglycylalanylleucine has: A) a disulfide bridge. B) five peptide bonds. C) four peptide bonds. D) no free carboxyl group. E) two free amino groups. 10. Peptides and proteins Page: 86 Difficulty: 1 Ans: C An octapeptide composed of four repeating glycylalanyl units has: A) one free amino group on an alanyl residue. B) one free amino group on an alanyl residue and one free carboxyl group on a glycyl residue. C) one free amino group on a glycyl residue and one free carboxyl group on an alanyl residue. D) two free amino and two free carboxyl groups. E) two free carboxyl groups, both on glycyl residues. 11. Peptides and proteins Page: 87 Difficulty: 2 Ans: B The average molecular weight of the 20 standard amino acids is 138, but biochemists use 110 when estimating the number of amino acids in a protein of known molecular weight. Why? A) The number 110 is based on the fact that the average molecular weight of a protein is 110,000 with an average of 1,000 amino acids. B) The number 110 reflects the higher proportion of small amino acids in proteins, as well as the loss of water when the peptide bond forms. C) The number 110 reflects the number of amino acids found in the typical small protein, and only small proteins have their molecular weight estimated this way. D) The number 110 takes into account the relatively small size of nonstandard amino acids. E) The number 138 represents the molecular weight of conjugated amino acids. 12. Peptides and proteins Page: 88 Difficulty: 1 Ans: B Which of the following refers to particularly stable arrangements of amino acid residues in a protein that give rise to recurring patterns? A) Primary structure B) Secondary structure C) Tertiary structure D) Quaternary structure E) None of the above 13. Peptides and proteins
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Chapter 1 The Foundations of Biochemistry
Page: 88 Difficulty: 1 Ans: D Which of the following describes the overall three-dimensional folding of a polypeptide? A) B) C) D) E) Primary structure Secondary structure Tertiary structure Quaternary structure None of the above
Short Answer Questions
14. Amino acids Page: 79 Difficulty: 1 Only one of the common amino acids has no free -amino group. Name this amino acid and draw its structure. Ans: The amino acid L-proline has no free -amino group, but rather has an imino group formed by cyclization of the R-group aliphatic chain with the amino group (see Fig. 3-5, p. 79). 15. Amino acids Pages: 7879 Difficulty: 2 Briefly describe the five major groupings of amino acids. Ans: Amino acids may be categorized by the chemistry of their R groups: (1) nonpolar aliphatics; (2) polar, uncharged; (3) aromatic; (4) positively charged; (5) negatively charged. (See Fig. 3-5, p. 79.) 16. Amino acids Pages: 7879 Difficulty: 2 A B C D E __________________________________________________________________ Tyr-Lys-Met Gly-Pro-Arg Asp-Trp-Tyr Asp-His-Glu Leu-Val-Phe Which one of the above tripeptides: ____(a) is most negatively charged at pH 7?
____(b) will yield DNP-tyrosine when reacted with l-fluoro-2,4-dinitrobenzene and hydrolyzed in acid?
____(c) contains the largest number of nonpolar R groups? ____(d) contains sulfur? ____(e) will have the greatest light absorbance at 280 nm? Ans: (a) D; (b) A; (c) E; (d) A; (e) C 17. Amino acids Page: 81 Difficulty: 1 Why do amino acids, when dissolved in water, become zwitterions? Ans: Near pH = 7, the carboxylic acid group (COOH) will dissociate to become a negatively charged COO group, and the NH2 amino group will attract a proton to become a positively
Chapter 1 The Foundations of Biochemistry
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charged NH3+ group. 18. Amino acids Page: 82 Difficulty: 1 As more OH equivalents (base) are added to an amino acid solution, what titration reaction will occur around pH = 9.5? Ans: Around pH = 9.5, the NH3+ group will be titrated according to the reaction: NH3+ + OH NH2 + H2O. 19. Amino acids Page: 84 Difficulty: 2 What is the pI, and how is it determined for amino acids that have nonionizable R groups? Ans: The pI is the isoelectric point. It occurs at a characteristic pH when a molecule has an equal number of positive and negative charges, or no net charge. For amino acids with nonionizable R groups, pI is the arithmetic mean of a molecules two pKa values: pI = 1/2 (pK1 + pK2) 20. Amino acids Page: 84 Difficulty: 2 The amino acid histidine has a side chain for which the pKa is 6.0. Calculate what fraction of the histidine side chains will carry a positive charge at pH 5.4. Be sure to show your work. Ans: pH = pKa + log
[ o j gt c nu ae [ cd ai ]
[acid] [conjugate base] [acid] [conjugate base] [acid] [conjugate base]
bs ] ae
pKa pH = log
antilog (pKa pH) =
antilog (6.0 5.4) =
4 = [acid]/[conjugate base], or 4[conjugate base] = [acid]
Therefore, at pH 5.4, 4/5 (80%) of the histidine will be in the protonated form.