CHEMISTRY THE CENTRAL SCIENCE

24 THE CHEMISTRY OF LIFE: ORGANIC AND BIOLOGICAL CHEMISTRY

EXERCISES

VISUALIZING CONCEPTS

24.1 All the structures shown here have the molecular formula C8H18. Which structures are the same molecule? (Hint: One way to answer this question is to determine the chemical name for each structure.) [Section 24.2]

24.2 Which of these molecules is unsaturated? [Section 24.3]

24.3 Which of these molecules most readily undergoes an addition reaction? [Section 24.3]

24.4 Which of these compounds would you expect to have the highest boiling point? Explain. [Section 24.4]

24.5 Which of these compounds can be a member of an isomer pair? In each case where isomerism is possible, identify the type or types of isomerism. [Sections 24.2, 24.4]

24.6 From examination of the molecular models i-v, choose the substance that (a) can be hydrolyzed to form a solution containing glucose, (b) is capable of forming a zwitterion, (c) is one of the four bases present in DNA, (d) reacts with an acid to form an ester, (e) is a lipid. [Sections 24.6–24.10]

INTRODUCTION TO ORGANIC COMPOUNDS; HYDROCARBONS (sections 24.1 and 24.2)

24.7 What are the characteristic hybrid orbitals employed by (a) carbon in an alkane, (b) carbon in a double bond in an alkene, (c) carbon in the benzene ring, (d) carbon in a triple bond in an alkyne?

24.8 What are the approximate bond angles (a) about carbon in an alkane, (b) about a doubly bonded carbon atom in an alkene, (c) about a triply bonded carbon atom in an alkyne?

24.9 Predict the ideal values for the bond angles about each carbon atom in the following molecule. Indicate the hybridization of orbitals for each carbon.

CH3CCCH2COOH

24.10 Identify the carbon atom(s) in the structure shown that has (have) each of the following hybridizations: (a) sp3(b) sp(c) sp2.

24.11 Are carbon monoxide or ammonia considered organic molecules? Why or why not?

24.12 Organic compounds containing C—O and C—Cl bonds are more reactive than simple alkane hydrocarbons. Considering the comparative values of C—H, C—C, C—O, and C—Cl bond enthalpies (Table 8.4), why is this so?

24.13 (a) What is the difference between a straight-chain and branched-chain alkane? (b) What is the difference between an alkane and an alkyl group?

24.14 What structural features help us identify a compound as (a) an alkane, (b) a cycloalkane, (c) an alkene, (d) an alkyne, (e) a saturated hydrocarbon, (f) an aromatic hydrocarbon?

24.15 Give the the name or condensed structural formula, as appropriate:

(c) 2-methylheptane

(d) 4-ethyl-2,3-dimethyloctane

(e) 1,2-dimethylcyclohexane

24.16 Give the name or condensed structural formula, as appropriate:

(c) 2,5,6-trimethylnonane

(d) 3-propyl-4,5-methyldecane

(e) 1-ethyl-3-methylcyclohexane

24.17 Give the name or condensed structural formula, as appropriate:

(b) 2,2-dimethylpentane

(c) 4-ethyl-1,1-dimethylcyclohexane

(d) (CH3)2CHCH2CH2C(CH3)3

(e) CH3CH2CH(C2H5)CH2CH2CH2CH3

24.18 Give the name or condensed structural formula, as appropriate:

(a) 3-phenylpentane

(b) 2,3-dimethylhexane

(c) 2-ethyl-2-methylhepane

(d) CH3CH2CH(CH3)CH2CH(CH3)2

24.19 What is the octane number of a mixture that is 35% heptane and 65% isooctane?

24.20 Describe two ways in which the octane number of a gasoline consisting of alkanes can be increased.

ALKENES, ALKYNES, AND AROMATIC HYDROCARBONS (section 24.3)

24.21 (a) Why are alkanes said to be saturated? (b) Is C4H6 a saturated hydrocarbon? Why or why not?

24.22 (a) Is the compound CH3CH=CH2 saturated or unsatu-rated? Explain. (b) What is wrong with the formula CH3CH2CH=CH3?

24.23 Give the molecular formula of a hydrocarbon containing five carbon atoms that is (a) an alkane, (b) a cycloalkane, (c) an alkene, (d) an alkyne. Which are saturated and which are un-saturated hydrocarbons?

24.24 Give the molecular formula of a cyclic alkane, a cyclic alkene, a linear alkyne, and an aromatic hydrocarbon that in each case contains six carbon atoms. Which are saturated and which are unsaturated hydrocarbons?

24.25 Enediynes are a class of compounds that include some antibiotic drugs. Draw the structure of an “enediyne” fragment that contains six carbons in a row. (Hint: di means “two.”)

24.26 Give the general formula for any cyclic alkene, that is, a cyclic hydrocarbon with one double bond.

24.27 Write the condensed structural formulas for as many alkenes and alkynes as you can think of that have the molecular formula C6H10.

24.28 Draw all the possible noncyclic structural isomers of C5H10. Name each compound.

24.29 Name or write the condensed structural formula for the following compounds:

(a) trans -2-pentene

(b) 2,5-dimethyl-4-octene

24.30 Name or write the condensed structural formula for the follow ing compounds:

(a) 4-methyl-2-pentene

(b) cis-2,5-dimethyl-3-hexene

(c) ortho-dimethylbenzene

(d) HC≡CCH2CH3

(e) trans-CH3CH═CHCH2CH2CH2CH3

24.31 Why is geometric isomerism possible for alkenes but not for alkanes and alkynes?

24.32 Draw all structural and geometric isomers of butene and name them.

24.33 Indicate whether each of the following molecules is capable of geometrical (cis-trans) isomerism. For those that are, draw the structures: (a) 1,1-dichloro-1-butene, (b) 2,4-dichloro-2-butene, (c) 1,4-dichlorobenzene, (d) 4,5-dimethyl-2-pentyne.

24.34 Draw the three distinct geometric isomers of 2,4-hexadiene.

24.35 (a) What is the difference between a substitution reaction and an addition reaction? Which one is commonly observed with alkenes and which one with aromatic hydrocarbons? (b) Using condensed structural formulas, write the balanced equation for the addition reaction of 2-pentene with Br2 and name the resulting compound. (c) Write a balanced chemical equation for the substitution reaction of Cl2 with benzene to make para-dichlorobenzene in the presence of FeCl3 as a catalyst.

24.36 Using condensed structural formulas, write a balanced chemical equation for each of the following reactions: (a) hydrogenation of cyclohexene; (b) addition of H2O to trans-2-pentene using H2SO4 as a catalyst (two products); (c) reaction of 2-chloropropane with benzene in the presence of AlCl3.

24.37 (a) When cyclopropane is treated with HI, 1-iodopropane is formed. A similar type of reaction does not occur with cy-clopentane or cyclohexane. How do you account for the reactivity of cyclopropane? (b) Suggest a method of preparing ethylbenzene, starting with benzene and ethylene as the only organic reagents.

24.38 (a) One test for the presence of an alkene is to add a small amount of bromine, a red-brown liquid, and look for the disappearance of the red-brown color. This test does not work for detecting the presence of an aromatic hydrocarbon. Explain. (b) Write a series of reactions leading to para-bromoethylbenzene, beginning with benzene and using other reagents as needed. What isomeric side products might also be formed?

24.39 The rate law for addition of Br2 to an alkene is first order in Br2 and first order in the alkene. Does this fact prove that the mechanism of addition of Br2 to an alkene proceeds in the same manner as for addition of HBr? Explain.

24.40 Describe the intermediate that is thought to form in the addition of a hydrogen halide to an alkene, using cyclohexene as the alkene in your description.

24.41 The molar heat of combustion of gaseous cyclopropane is –2089 kJ/mol; that for gaseous cyclopentane is –3317 kJ/mol. Calculate the heat of combustion per CH2 group in the two cases, and account for the difference.

24.42 The heat of combustion of decahydronaphthalene (C10H18) is –6286 kJ/mol. The heat of combustion of naphthalene (C10H8) is –5157 kJ/mol. [In both cases CO2(g) and H2O(l) are the products.] Using these data and data in Appendix C, calculate the heat of hydrogenation of naphthalene. Does this value provide any evidence for aromatic character in naphthalene?

FUNCTIONAL GROUPS AND CHIRALITY (sections 24.4 and 24.5)

24.43 Identify the functional groups in each of the following compounds:

(a) H3C—CH2—OH

(e) CH3CH2CH2CH2CHO

24.44 Identify the functional groups in each of the following compounds:

24.45 Give the structural formula for (a) an aldehyde that is an iso-mer of acetone, (b) an ether that is an isomer of 1-propanol.

24.46 (a) Give the empirical formula and structural formula for a cyclic ether containing four carbon atoms in the ring. (b) Write the structural formula for a straight-chain compound that is a structural isomer of your answer to part (a).

24.47 The IUPAC name for a carboxylic acid is based on the name of the hydrocarbon with the same number of carbon atoms. The ending -oic is appended, as in ethanoic acid, which is the IUPAC name for acetic acid. Draw the structure of the following acids: (a) methanoic acid, (b)pentanoic acid, (c) 2-chloro-3-methyldecanoic acid.

24.48 Aldehydes and ketones can be named in a systematic way by counting the number of carbon atoms (including the carbonyl carbon) that they contain. The name of the aldehyde or ketone is based on the hydrocarbon with the same number of carbon atoms. The ending -al for aldehyde or -one for ketone is added as appropriate. Draw the structural formulas for the following aldehydes or ketones: (a) propanal, (b) 2-pentanone, (c) 3-methyl-2-butanone, (d) 2-methylbutanal.

24.49 Draw the condensed structure of the compounds formed by condensation reactions between (a) benzoic acid and ethanol, (b) ethanoic acid and methylamine, (c) acetic acid and phenol. Name the compound in each case.

24.50 Draw the condensed structures of the compounds formed from (a) butanoic acid and methanol, (b) benzoic acid and 2-propanol, (c) propanoic acid and dimethylamine. Name the compound in each case.

24.51 Write a balanced chemical equation using condensed structural formulas for the saponification (base hydrolysis) of (a) methyl propionate, (b) phenyl acetate.

24.52 Write a balanced chemical equation using condensed structural formulas for (a) the formation of butyl propionate from the appropriate acid and alcohol, (b) the saponification (base hydrolysis) of methyl benzoate.

24.53 Would you expect pure acetic acid to be a strongly hydrogen-bonded substance? How do the melting and boiling points of the substance (16.7 °C and 118 °C) support your answer?

24.54 Acetic anhydride is formed from acetic acid in a condensation reaction that involves the removal of a molecule of water from between two acetic acid molecules. Write the chemical equation for this process, and show the structure of acetic anhydride.

24.55 Write the condensed structural formula for each of the following compounds: (a) 2-pentanol, (b) 1,2-propanediol, (c) ethyl acetate, (d) diphenyl ketone, (e) methyl ethyl ether.

24.56 Write the condensed structural formula for each of the following compounds: (a) 2-ethyl-1-hexanol, (b) methyl phenyl ketone, (c) para-bromobenzoic acid, (d) ethyl butyl ether, (e) N, N-dimethylbenzamide.

24.57 Draw the structure for 2-bromo-2-chloro-3-methylpentane, and indicate any chiral carbons in the molecule.

24.58 Does 3-chloro-3-methylhexane have optical isomers? Why or why not?

PROTEINS (section 24.7)

24.59 (a) What is an α-amino acid? (b) How do amino acids react to form proteins? (c) Draw the bond that links amino acids together in proteins. What is this called?

24.60 What properties of the side chains (R groups) of amino acids are important in affecting the amino acids' overall biochemical behavior? Give examples to illustrate your reply.

24.61 Draw the two possible dipeptides formed by condensation reactions between leucine and tryptophan.

24.62 Write a chemical equation for the formation of methionyl glycine from the constituent amino acids.

24.63 (a) Draw the condensed structure of the tripeptide Gly-Gly-His. (b) How many different tripeptides can be made from the amino acids glycine and histidine? Give the abbreviations for each of these tripeptides, using the three-letter and one-letter codes for the amino acids.

24.64 (a) What amino acids would be obtained by hydrolysis of the following tripeptide?

(b) How many different tripeptides can be made from glycine, serine, and glutamic acid? Give the abbreviation for each of these tripeptides, using the three-letter codes and one-letter codes for the amino acids.

24.65 (a) Describe the primary, secondary, and tertiary structures of proteins. (b) Quaternary structures of proteins arise if two or more smaller polypeptides or proteins associate with each other to make an overall much larger protein structure. The association is due to the same hydrogen bonding, electrostatic, and dispersion forces we have seen before. Hemoglobin, the protein used to transport oxygen molecules in our blood, is an example of a protein that has quaternary structure. Hemoglobin is a tetramer; it is made of four smaller polypeptides, two “alphas” and two “betas.” (These names do not imply anything about the number of alpha-helices or beta sheets in the individual polypeptides.) What kind of experiments would provide sound evidence that hemoglobin exists as a tetramer and not as one enormous polypeptide chain? You may need to look into the chemical literature to discover techniques that chemists and biochemists use to make these decisions.

24.66 What is the difference between the α-helix and β-sheet secondary structures in proteins?

CARBOHYDRATES AND LIPIDS (sections 24.8 and 24.9)

24.67 In your own words, define the following terms: (a) carbohydrate, (b) monosaccharide, (c) disaccharide, (d) polysaccharide.

24.68 What is the difference between α-glucose and β-glucose? Show the condensation of two glucose molecules to form a disaccharide with an a linkage; with a β linkage.

24.69 What is the empirical formula of cellulose? What is the unit that forms the basis of the cellulose polymer? What form of linkage joins these monomeric units?

24.70 What is the empirical formula of glycogen? What is the unit that forms the basis of the glycogen polymer? What form of linkage joins these monomeric units?

24.71 The structural formula for the linear form of D-mannose is

(a) How many chiral carbons are present in the molecule? (b) Draw the structure of the six-member-ring form of this sugar.

24.72 The structural formula for the linear form of galactose is

(a) How many chiral carbons are present in the molecule? (b) Draw the structure of the six-member-ring form of this sugar.

24.73 Describe the chemical structures of lipids and phospholipids. Why can phospholipids form a bilayer in water?

24.74 Using data from Table 8.4 on bond enthalpies, show that the more C—H bonds a molecule has compared to C—O and O—H bonds, the more energy it can store.

NUCLEIC ACIDS (section 24.10)

24.75 Adenine and guanine are members of a class of molecules known as purines; they have two rings in their structure. Thymine and cytosine, on the other hand, are pyrimidines, and have only one ring in their structure. Predict which have larger dispersion forces in aqueous solution, the purines or the pyrimidines.

24.76 A nucleoside consists of an organic base of the kind shown in Section 24.10, bound to ribose or deoxyribose. Draw the structure for deoxyguanosine, formed from guanine and deoxyribose.

24.77 Just as the amino acids in a protein are listed in the order from the amine end to the carboxylic acid end (the protein sequence), the bases in nucleic acids are listed in the order 5' to 3', where the numbers refer to the position of the carbons in the sugars (shown here for deoxyribose):

The base is attached to the sugar at the 1' carbon. The 5' end of a DNA sequence is a phosphate of an OH group, and the 3' end of a DNA sequence is the OH group. What is the DNA sequence for the molecule shown here?

24.78 When samples of double-stranded DNA are analyzed, the quantity of adenine present equals that of thymine. Similarly, the quantity of guanine equals that of cytosine. Explain the significance of these observations.

24.79 Imagine a single DNA strand containing a section with the following base sequence: 5'-GCATTGGC-3'. What is the base sequence of the complementary strand? (The two strands of DNA will come together in an antiparallel fashion; that is, 5'-TAG-3' will bind to 3'-ATC-5'.)

24.80 Explain the chemical differences between DNA and RNA.

ADDITIONAL EXERCISES

24.81 Draw the condensed structural formulas for two different molecules with the formula C3H4O.

24.82 How many structural isomers are there for a five-member straight carbon chain with one double bond? For a six-member straight carbon chain with two double bonds?

24.83 Draw the condensed structural formulas for the cis and trans isomers of 2-pentene. Can cyclopentene exhibit cis-trans iso-merism? Explain.

24.84 If a molecule is an “ene-one,” what functional groups must it have?

24.85 Write the structural formulas for as many alcohols as you can think of that have empirical formula C3H6O.

24.86 Identify each of the functional groups in these molecules:

24.87 Write a condensed structural formula for each of the following: (a) an acid with the formula C4H8O2(b) a cyclic ketone with the formula C5H8O, (c) a dihydroxy compound with the formula C3H8O2(d) a cyclic ester with the formula C5H8O2.

24.88 Although carboxylic acids and alcohols both contain an—OH group, one is acidic in water and the other is not. Explain the difference.

[24.89] Indole smells terrible in high concentrations but has a pleasant floral-like odor when highly diluted. Its structure is

The molecule is planar, and the nitrogen is a very weak base, with Kb = 2 × 10–12. Explain how this information indicates that the indole molecule is aromatic.

24.90 Locate the chiral carbon atoms, if any, in each molecule:

24.91 Which of the following peptides have a net positive charge at pH 7? (a) Gly-Ser-Lys, (b) Pro-Leu-Ile, (c) Phe-Tyr-Asp.

24.92 Glutathione is a tripeptide found in most living cells. Partial hydrolysis yields Cys-Gly and Glu-Cys. What structures are possible for glutathione?

24.93 Monosaccharides can be categorized in terms of the number of carbon atoms (pentoses have five carbons and hexoses have six carbons) and according to whether they contain an aldehyde (aldo- prefix, as in aldopentose) or ketone group (keto- prefix, as in ketopentose). Classify glucose and fructose in this way.

24.94 Can a DNA strand bind to a complementary RNA strand? Explain.

INTEGRATIVE EXERCISES

24.95 Explain why the boiling point of ethanol (78 °C) is much higher than that of its isomer, dimethyl ether (–25 °C), and why the boiling point of CH2F2 (–52 °C) is far above that of CH4 (–128 °C).

[24.96] An unknown organic compound is found on elemental analysis to contain 68.1% carbon, 13.7% hydrogen, and 18.2% oxygen by mass. It is slightly soluble in water. Upon careful oxidation it is converted into a compound that behaves chemically like a ketone and contains 69.7% carbon, 11.7% hydrogen, and 18.6% oxygen by mass. Indicate two or more reasonable structures for the unknown.

24.97 An organic compound is analyzed and found to contain 66.7% carbon, 11.2% hydrogen, and 22.1% oxygen by mass. The compound boils at 79.6 °C. At 100 °C and 0.970 atm, the vapor has a density of 2.28 g/L. The compound has a carbonyl group and cannot be oxidized to a carboxylic acid. Suggest a structure for the compound.

[24.98] An unknown substance is found to contain only carbon and hydrogen. It is a liquid that boils at 49 °C at 1 atm pressure. Upon analysis it is found to contain 85.7% carbon and 14.3% hydrogen by mass. At 100 °C and 735 torr, the vapor of this unknown has a density of 2.21 g/L. When it is dissolved in hexane solution and bromine water is added, no reaction occurs. What is the identity of the unknown compound?

24.99 The standard free energy of formation of solid glycine is –369 kJ/mol, whereas that of solid glycylglycine is –488 kJ/mol. What is ΔG° for the condensation of glycine to form glycylglycine?

24.100 A typical amino acid with one amino group and one car-boxylic acid group, such as serine (Figure 24.18), can exist in water in several ionic forms. (a) Suggest the forms of the amino acid at low pH and at high pH. (b) Amino acids generally have two pKa values, one in the range of 2 to 3 and the other in the range of 9 to 10. Serine, for example, has pKa values of 2.19 and 9.21. Using species such as acetic acid and ammonia as models, suggest the origin of the two pKa values. (c) Glutamic acid is an amino acid that has three pKa's: 2.10, 4.07, and 9.47. Draw the structure of glutamic acid, and assign each pKa to the appropriate part of the molecule.

[24.101] The protein ribonuclease A in its native, or most stable, form is folded into a compact globular shape:

(a) Does the native form have a lower or higher free energy than the denatured form, in which the protein is an extended chain? (b) What is the sign of the entropy change in going from the denatured to the folded form? (c) In the native form, the molecule has four—S—S—bonds that bridge parts of the chain. What effect do you predict these four linkages to have on the free energy and entropy of the native form relative to the free energy and entropy of a hypothetical folded structure that does not have any—S—S—linkages? Explain. (d) A gentle reducing agent converts the four—S—S—linkages in ribonuclease A to eight—S—H bonds. What effect do you predict this conversion to have on the tertiary structure and entropy of the protein? (e) Which amino acid must be present for SH bonds to exist in ribonuclease A?

24.102 The monoanion of adenosine monophosphate (AMP) is an intermediate in phosphate metabolism:

where A = adenosine. If the pKa for this anion is 7.21, what is the ratio of [AMP—OH] to [AMP—O2–] in blood at pH 7.4?