Chapter 1 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

they can form. 6. 9. rather than covalent. (b) Because noncovalent interactions are weak. Chemical foundations Pages: 17. E) heterotrophic. how many amino acids are in the protein. Short Answer Questions 8. the sequence of amino acids in the protein. 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. C) increasing the activation energy. B) anabolic. E) increasing the energy of the transition state. hydrophobic interaction with lipids that provide a folding framework. D) increasing the amount of free energy released. Physical foundations Page: 27 Difficulty: 1 Ans: B Energy requiring metabolic pathways that yield complex molecules from simpler precursors are: A) A) amphibolic. modification during interactions with ribosomes. 10. (b) Why is it important that these interactions be noncovalent. van der Waals interactions. ionic interactions between charged groups. 20 Difficulty: 3 Differentiate between configuration and conformation. break. B) decreasing the amount of free energy released. 7. Ans: Configuration denotes the spatial arrangement of the atoms of a molecule that is conferred by . D) catabolic. which may be distinguishable from one another in a biological system. bonds? Ans: (a) Noncovalent interactions include hydrogen bonds. and cannot be superimposed on its mirror image—as a right hand cannot fit into a left glove. and re-form more rapidly and with less energy input than can covalent bonds.2 Chapter 1 The Foundations of Biochemistry Enzymes are biological catalysts that enhance the rate of a reaction by: decreasing the activation energy. Thus a molecule with one chiral carbon will have two stereoisomers. C) autotrophic. 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. 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 hydrophobic interactions. This is important to maintain the flexibility needed in macromolecules.

he was able to separate the two types of crystals found in tartaric acid (racemic acid) that are identical in shape. which give rise to stereoisomers. the other toxic. How. One sample rotated polarized light to the left. are free to assume different positions in space because of the freedom of bond rotation. then. label the transition state and the overall freeenergy change (∆ G) for the uncatalyzed reaction A → B. the mirror image crystals rotated polarized light to the right. Chemical foundations Pages: 20-21 Difficulty: 3 A chemist working in a pharmaceutical lab synthesized a new drug as a racemic mixture. One may be beneficial. do cells accomplish this process? Ans: The endergonic (thermodynamically unfavorable) reaction is coupled to an exergonic (thermodynamically favorable) reaction through a shared intermediate. Physical foundations Pages: 26-27 Difficulty: 2 (a) On the reaction coordinate diagram shown below. 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. without breaking any bonds. . (b) Is this an exergonic or endergonic reaction? (c) Draw a second curve showing the energetics of the reaction if it were enzymecatalyzed. Conformation refers to the spatial arrangement of substituent groups that.Chapter 1 The Foundations of Biochemistry 3 the presence of either double bonds. or one enantiomer may be ineffective and its presence could reduce the efficacy of the other enantiomer. so each of the two enantiomers of the drug may have very different effects on an organism. 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 that the overall free-energy change of the coupled reactions is negative (the overall reaction is exergonic). 13. 11. 12. but mirror images of each other. or chiral centers. 14. 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. Configurational isomers can only be interconverted by temporarily breaking covalent bonds. (b) Using fine forceps. around which there is no freedom of rotation. Chemical foundations Pages: 17.

C) is a hydrated proton. D) three-dimensional folding of a polypeptide chain. 27. B) enzyme-substrate interactions.4 Chapter 1 The Foundations of Biochemistry Ans: (a) and (c) (See Fig. Weak interactions in aqueous systems Page: 53–54 Difficulty: 2 Ans: E Hydrophobic interactions make important energetic contributions to: A) binding of a hormone to its receptor protein. E) primarily involve the effect of polar solutes on the entropy of aqueous systems. D) Individual hydrogen bonds in liquid water exist for many seconds and sometimes for minutes. 3. C) membrane structure. E) all of the above are true. 1-27. Ionization of water. and weak bases Page: 60 Difficulty: 2 Ans: E A hydronium ion: A) has the structure H3O+. weak acids. 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. 4. B) is a hydrated hydrogen ion. D) involve the ability of water to denature proteins. B) do not contribute to the structure of water-soluble proteins. p. 2. E) all of the above are true. C) Individual hydrogen bonds are much weaker than covalent bonds. Ionization of water. E) The strength of a hydrogen bond depends on the linearity of the three atoms involved in the bond. and weak bases Page: 61 Difficulty: 2 Ans: A The pH of a solution of 1 M HCl is: . the average water molecule forms hydrogen bonds with three to four other water molecules. Weak interactions in aqueous systems Page: 47–49 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. weak acids.) (b) exergonic reaction Chapter 2 Water Multiple Choice Questions 1. D) is the usual form of one of the dissociation products of water in solution. B) In liquid water. C) have bonding energies of approximately 20–40 Kjoule per mole. 5.

4. C) 0. Ionization of water.75). and 12. C) HPO42–. Ionization of water. weak acids. 6.86. D) PO43–. B) A pH change from 8. with pKa’s of 2. and weak bases Page: 63 Difficulty: 1 Ans: D The aqueous solution with the lowest pH is: A) 0. 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. B) H2PO4–.000 times lower [H+] than the gastric juice. E) 10–12 M NaOH. the salt concentration is higher than that of the acid. 9. D) 6. 10. 7.0 reflects an increase in the hydroxide ion concentration ([OH-]) of 20%. 8. and weak bases Page: 63 Difficulty: 2 Ans: B Phosphoric acid is tribasic.1 C) 1 D) 10 E) –1 6. C) Charged molecules are generally insoluble in water.1 M acetic acid (pKa = 4.86). D) 0. The ionic form that predominates at pH 3. Ionization of water.0 to 6. C) 6 times lower [H+] than the gastric juice. weak acids.4. and weak bases Page: 62 Difficulty: 2 Ans: E The pH of a sample of blood is 7. Buffering against pH changes in biological systems Page: 65–66 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. Ionization of water. E) a million times lower [H+] than the gastric juice. weak acids.2 is: A) H3PO4. B) 0.14.1 M HCl.Chapter 1 The Foundations of Biochemistry 5 A) 0 B) 0. .4. B) 5. E) The pH can be calculated by adding 7 to the value of the pOH. D) Hydrogen bonds form readily in aqueous solutions.1 M formic acid (pKa = 3. The blood sample has: A) 0. E) none of the above.01 M HCl.189 times the [H+] as the gastric juice.29 times lower [H+] than the gastric juice. At pH values lower than the pKa.0 reflects a decrease in the proton concentration ([H+]) by a factor of 100. while gastric juice is pH 1. weak acids.

5 12. D) ratio of acetic acid to sodium acetate in the buffer falls. Buffering against pH changes in biological systems Page: 65–67 Difficulty: 3 Ans: D A compound has a pKa of 7. C) pH rises more than if an equal amount of NaOH is added to unbuffered water at pH 4. D) The strongest buffers are those composed of strong acids and strong bases. Buffering against pH changes in biological systems Page: 66–67 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.5 B) 6. E) When pH = pKa. initially at the same pH as its pKa (4.4. The resulting solution is pH: A) 6.8 C) 7. B) does not explain the behavior of di. To 100 mL of a 1.2 D) 7. 13. 14. 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.76). E) relates the pH of a solution to the pKa and the concentrations of acid and conjugate base. When sodium hydroxide (NaOH) is mixed with this buffer. the: A) pH remains constant. 11.76.0 is added 30 mL of 1. B) pH rises more than if an equal amount of NaOH is added to an acetate buffer initially at pH 6. E) sodium acetate formed precipitates because it is less soluble than acetic acid.76. . D) is equally useful with solutions of acetic acid and of hydrochloric acid.or tri-basic weak acids C) employs the same value for pKa for all weak acids. the weak acid and salt concentrations in a buffer are equal.0 M solution of this compound at pH 8. Buffering against pH changes in biological systems Page: 66–67 Difficulty: 2 Ans: D Consider an acetate buffer.0 M hydrochloric acid.6 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.4 E) 7. 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.

RNH2. reducing the total area of the two groups that is exposed to surrounding molecules of the polar solvent (water). Which form of phosphoric acid predominates in a solution at pH 4? Explain your answer. (2) electrostatic interactions: relatively weak charge-charge interactions (attractions of opposite charges. 2-16). Buffering against pH changes in biological systems Page: 64–66 Difficulty: 2 Give the general Henderson-Hasselbalch equation and sketch the plot it describes (pH against amount of NaOH added to a weak acid). Acid pKa H3PO4 2. Short Answer Questions 15.14) has been titrated completely. Ionization of water. the form with one dissociated proton (see Fig. circle the conjugate base. 18. weak acids. The dominant form at pH 4 is therefore H2PO4–. Weak interactions in aqueous systems Page: 47–55 Difficulty: 2 Name and briefly define four types of noncovalent interactions that occur between biological molecules. HCO3– 17. (4) van der Waals interactions: weak interactions between the electric dipoles that two close-spaced atoms induce in each other.86 12. Ans: The inflection point. 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. and weak bases Page: 63 Difficulty: 1 For each of the pairs below. On your curve label the pKa for the weak acid. RCOOH RNH2 H2PO4– H2CO3 RCOO– RNH3+ H3PO4 HCO3– Ans: RCOO–. the first dissociable proton (pKa = 2. and the second (pKa = 6.86) has just started to be titrated. and weak bases Page: 63 Difficulty: 2 Phosphoric acid (H3PO4) has three dissociable protons. The region of greatest buffering capacity . (3) hydrophobic interactions: the forces that tend to bring two hydrophobic groups together.Chapter 1 The Foundations of Biochemistry 7 E) None of the above.14 H2PO4– HPO42– 6. occurs at a pH equal to the pKa of the weak acid. which occurs when the weak acid has been exactly one half titrated with NaOH. Ionization of water.4 Ans: At pH 4. with the pKa’s shown below. weak acids. and indicate the region in which the buffering capacity of the system is greatest. H2PO4–. repulsions of like charges) between two ionized groups. 16.

2. 2-18. From the Henderson-Hasselbalch equation. whose pKa is 3. with the midpoint of the titration (inflection point) at pH 3. 65.7 – 0. HA.) Ans: Addition of 200 mmol of NaOH (400 mL × 0. 65. show how you would calculate the ratio of acid to salt at pH 5.7 + log (0.5 mol of acetic acid per liter to 400 mL of 0. p.5 mM) completely titrates the acid so that it can no longer act as a buffer and leaves 150 mmol of .0.68 20. Ans: 23.1/0. What is the pH of the resulting solution? Ans: pH = pKa + log [ c o n j u g a t e [ a c i d ] b a s e ] = 4. added base should have the general shape of those shown in Fig.22 22.2 + 0. What is the pH at this point? Ans: The plot of pH vs.7 + log (5/150) = 4.) 19.1 M sodium acetate? Ans: pH = pKa + log [ c o n j u g a t e [ a c i d ] b a s e ] = 4. Buffering against pH changes in biological systems Page: 65 Difficulty: 3 Draw the titration curve for a weak acid.4 21. The ratio of A– to HA is 3 when 0. (See Fig.7) and 0.7). 2-18. the pH at this point can be calculated: pH = pKa + log [ c o n j u g a t e [ a c i d ] b a s e ] = 3.75 equivalents of base have been added.5 M NaOH.5 M) to 50 mmol of acetic acid (100 mL × 0.3 = 4. p.48 = 3.7 – 1. What is the final pH? (The pKa of acetic acid is 4.1 M sodium acetate solution with 150 mL of 1 M acetic acid (pKa = 4.2 M acetic acid (pKa = 4.8 Chapter 1 The Foundations of Biochemistry (where the titration curve is flattest) occurs at pH values of pKa ±1. Buffering against pH changes in biological systems Page: 66–67 Difficulty: 2 You have just made a solution by combining 50 mL of a 0. Buffering against pH changes in biological systems Page: 66–67 Difficulty: 2 What is the pH of a solution containing 0. Buffering against pH changes in biological systems Page: 66–67 Difficulty: 2 For a weak acid with a pKa of 6.2 + log 3 = 3. Label the axes properly. Buffering against pH changes in biological systems Page: 66-67 Difficulty: 3 Suppose you have just added 100 mL of a solution containing 0.2.7.48 = 3.2) = 4. Indicate with an arrow where on the curve the ratio of salt (A–) to acid (HA) is 3:1.

1 mol of salt. contains only nitrogen E) proline. by definition.3 M pH is. Given [OH–]. only ___________ is not optically active.9 mol of weak acid and 0.Chapter 1 The Foundations of Biochemistry 9 NaOH dissolved in 500 mL. forms a covalent bond with the amino group 3. D) is in the L absolute configuration in naturally occurring proteins. A) alanine. has a pKa of 5. is a simple methyl group B) glycine.0. 24. log (1/[H+]) pH = log (0. Amino acids Page: 76 Difficulty: 2 Ans: B Of the 20 standard amino acids.05 Chapter 3 Amino Acids. A) B) . B) carbonyl group.1 mol of NaOH were dissolved in one liter of water. Buffering against pH changes in biological systems Page: 66-67 Difficulty: 2 A weak acid HA. The reason is that its side chain ___________.3 M /10–14 M2) = 12.3 M. E) is symmetric.0 mol of this acid and 0. is a carboxylic acid. is unbranched D) lysine. pH = pKa + log [ c o n j u g a t e [ a c i d ] b a s e ] = 5.0 + log (0. is a hydrogen atom C) glycine. and Proteins Multiple Choice Questions 1. [H+] can be calculated from the water constant: [H+][OH–] = 10–14 [H+] = 10–14 M2 / 0.9) = 4. except for proline. an [OH–] of 0. C) is bonded to four different chemical groups. Peptides. 2. Amino acids Page: 76 Difficulty: 1 Ans: C The chirality of an amino acid results from the fact that its α carbon: has no net charge. contain a(n): A) amino group. Amino acids Page: 79 Difficulty: 1 Ans: A All of the amino acids that are found in proteins.1/0. If 1.48.1 mol of NaOH yields 0. what would the final pH be? Ans: Combining 1 mol of weak acid with 0.

for example NaOH. D) The major contribution to the characteristic absorption of light at 280 nm by proteins is the phenylalanine R group. − B) —COOH + —NH2 → —COO + —NH2+. Amino acids Page: 84 Difficulty: 2 Ans: B For amino acids with neutral R groups. the population of amino acids in solution will have: − − . 4. 7. reveals two pK’s. Amino acids Pages: 82–83 Difficulty: 2 Ans: D Titration of valine by a strong base. B) Histidine’s ring structure results in its being categorized as aromatic or basic. C) polar or a nonpolar molecule. The titration reaction occurring at pK2 (pK2 = 9. Amino acids Page: 80 Difficulty: 2 Ans: A Which of the following statements about cystine is correct? Cystine forms when the —CH2—SH R group is oxidized to form a —CH2—S—S—CH2 — disulfide bridge between two cysteines. Amino acids Pages: 79–80 Difficulty: 3 Ans: C Which of the following statements about aromatic amino acids is correct? A) All are strongly hydrophilic. 6. E) transparent or a light-absorbing compound.62) is: A) —COOH + OH → —COO + H2O.10 Chapter 1 The Foundations of Biochemistry C) carboxyl group. D) Cystine is formed through a peptide linkage between two cysteines. at any pH below the pI of the amino acid. B) neutral molecule or an ion. E) The presence of a ring structure in its R group determines whether or not an amino acid is aromatic. D) ester group. 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. tryptophan absorbs more ultraviolet light than tyrosine. − + D) —NH3 + OH → —NH2 + H2O. C) Cystine is formed by the oxidation of the carboxylic acid group on cysteine. E) thiol group. B) Cystine is an example of a nonstandard amino acid. E) Two cystines are released when a —CH2—S—S—CH2— disulfide bridge is reduced to —CH2—SH. 8. D) standard or a nonstandard monomer in proteins. − C) —COO + —NH2+ → —COOH + —NH2. 5. depending on pH. − − E) —NH2 + OH → —NH + H2O. derived by linking two standard amino acids. C) On a molar basis.

but biochemists use 110 when estimating the number of amino acids in a protein of known molecular weight. D) The number 110 takes into account the relatively small size of nonstandard amino acids.Chapter 1 The Foundations of Biochemistry 11 A) a net negative charge.000 amino acids. Peptides and proteins Page: 86 Difficulty: 1 Ans: C The peptide alanylglutamylglycylalanylleucine has: A) a disulfide bridge. C) no charged groups. 10. E) positive and negative charges in equal concentration. C) one free amino group on a glycyl residue and one free carboxyl group on an alanyl residue. 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. E) two free amino groups. 11. D) no free carboxyl group. 12. and only small proteins have their molecular weight estimated this way. Peptides and proteins . B) The number 110 reflects the higher proportion of small amino acids in proteins. D) no net charge. B) five peptide bonds. Peptides and proteins Page: 87 Difficulty: 2 Ans: B The average molecular weight of the 20 standard amino acids is 138. D) two free amino and two free carboxyl groups. C) four peptide bonds. 9. E) The number 138 represents the molecular weight of conjugated amino acids. C) The number 110 reflects the number of amino acids found in the typical small protein. 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. both on glycyl residues. B) one free amino group on an alanyl residue and one free carboxyl group on a glycyl residue. Why? A) The number 110 is based on the fact that the average molecular weight of a protein is 110. B) a net positive charge. E) two free carboxyl groups.000 with an average of 1. as well as the loss of water when the peptide bond forms.

but rather has an imino group formed by cyclization of the R-group aliphatic chain with the amino group (see Fig. (d) A. 3-5. 15. Name this amino acid and draw its structure.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. Amino acids Pages: 78–79 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. become zwitterions? Ans: Near pH = 7. uncharged. Amino acids Page: 79 Difficulty: 1 Only one of the common amino acids has no free α -amino group. p.) 16. when dissolved in water. (b) A. (See Fig. Ans: The amino acid L-proline has no free α -amino group. (e) C 17. (2) polar. 79. Amino acids Pages: 78–79 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) positively charged. Amino acids Page: 81 Difficulty: 1 Why do amino acids. (c) E. 79). 3-5. the carboxylic acid group (—COOH) will dissociate to become a negatively charged —COO– group. (5) negatively charged. (3) aromatic. p. and the —NH2 amino group will attract a proton to become a positively .12 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.

what titration reaction will occur around pH = 9. Calculate what fraction of the histidine side chains will carry a positive charge at pH 5. 19.0. 18.4) = 4 = [acid]/[conjugate base].0 – 5. Amino acids Page: 84 Difficulty: 2 What is the pI.Chapter 1 The Foundations of Biochemistry 13 charged —NH3+ group. at pH 5.4. . Amino acids Page: 84 Difficulty: 2 The amino acid histidine has a side chain for which the pKa is 6. or no net charge. Ans: pH = pKa + log [ c o n j u g a t e [ a c i d ] [acid] [conjugate base] [acid] [conjugate base] [acid] [conjugate base] b a s e ] pKa – pH = log antilog (pKa – pH) = antilog (6. It occurs at a characteristic pH when a molecule has an equal number of positive and negative charges. pI is the arithmetic mean of a molecule’s two pKa values: pI = 1/2 (pK1 + pK2) 20. For amino acids with nonionizable R groups. the —NH3+ group will be titrated according to the reaction: —NH3+ + OH– → —NH2 + H2O. Be sure to show your work. and how is it determined for amino acids that have nonionizable R groups? Ans: The pI is the isoelectric point. Amino acids Page: 82 Difficulty: 1 As more OH– equivalents (base) are added to an amino acid solution.4. or 4[conjugate base] = [acid] Therefore. 4/5 (80%) of the histidine will be in the protonated form.5.5? Ans: Around pH = 9.

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