Chapter 25

Imagine a single DNA strand containing a section with the following base sequence: \(5^{\prime}\) -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, \(5^{\prime}-\mathrm{TAG}-3^{\prime}\) will bind to \(3^{\prime}-\mathrm{ATC}-5^{\prime} .\) )

Explain the chemical differences between DNA and RNA.

Draw the condensed structural formulas for two different molecules with the formula \(\mathrm{C}_{3} \mathrm{H}_{4} \mathrm{O}\).

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

There are no known stable cyclic compounds with ring sizes of seven or less that have an alkyne linkage in the ring. Why is this? Could a ring with a larger number of carbon atoms accommodate an alkyne linkage? Explain.

Although there are silicon analogs of alkanes, silicon analogs of alkenes or alkynes are virtually unknown. Suggest an explanation.

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

Write the structural formulas for as many alcohols as you can think of thathave empirical formula \(\mathrm{C}_{3} \mathrm{H}_{6} \mathrm{O}\).

Dinitromethane, \(\mathrm{CH}_{2}\left(\mathrm{NO}_{2}\right)_{2}\), is a dangerously reactive substance that decomposes readily on warming. On the other hand, dichloromethane is relatively unreactive. Why is the nitro compound so reactive compared to the chloro compound? (Hint: Consider the oxidation numbers of the atoms involved and the possible products of decomposition.)

Write a condensed structural formula for each of the following: (a) an acid with the formula \(\mathrm{C}_{4} \mathrm{H}_{8} \mathrm{O}_{2}\), (b) a cyclic ketone with the formula \(\mathrm{C}_{5} \mathrm{H}_{8} \mathrm{O}\), (c) a dihydroxy compound with formula \(\mathrm{C}_{3} \mathrm{H}_{8} \mathrm{O}_{2}\), (d) a cyclic ester with formula \(\mathrm{C}_{5} \mathrm{H}_{8} \mathrm{O}_{2}\)

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

Indole smells rather terrible in high concentrations but has a pleasant floral-like odor when highly diluted. It has the following structure: Indole is a planar molecule. The nitrogen is a very weak base, with a \(K_{b}\) of \(2 \times 10^{-12}\). Explain how this information indicates that the indole molecule is aromatic in character.

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

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

Starch, glycogen, and cellulose are all polymers of glucose. What are the structural differences among them?

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.

Can a DNA strand bind to a complementary RNAstrand? Explain.

Explain why the boiling point of ethanol \(\left(78^{\circ} \mathrm{C}\right)\) is much higher than that of its isomer, dimethyl ether \(\left(-25^{\circ} \mathrm{C}\right)\) and why the boiling point of \(\mathrm{CH}_{2} \mathrm{~F}_{2}\left(-52{ }^{\circ} \mathrm{C}\right)\) is far above that of \(\mathrm{CH}_{4}\left(-128^{\circ} \mathrm{C}\right)\).

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.

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 \(79.6^{\circ} \mathrm{C}\). At \(100{ }^{\circ} \mathrm{C}\) and \(0.970 \mathrm{~atm}\), the vapor has a density of \(2.28 \mathrm{~g} / \mathrm{L}\). The compound has a carbonyl group and cannot be oxidized to a carboxylic acid. Suggest a structure for the compound.

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

The standard freeenergy of formation of solid glycine is \(-369 \mathrm{~kJ} / \mathrm{mol}\), whereas that of solid glycylglycine is \(-488 \mathrm{~kJ} / \mathrm{mol}\). What is \(\Delta G^{\circ}\) for the condensation of glycine to form glycylglycine?

One of the most important molecules in biochemical systems is adenosine triphosphate (ATP), for which the structure is ATP is the principal carrier of biochemical energy. It is considered an energy-rich compound because the hydrolysis of ATP to yield adenosine diphosphate (ADP) and inorganic phosphate is spontaneous underaqueous biochemical conditions. (a) Write a balanced equation for the reaction of ATP with water to yield ADP and inorganic phosphate ion. [Hint: Hydrolysis reactions are just the reverse of condensation reactions(Section 22.8).] (b) What would you expect for the sign of the free-energy change for this reaction? (c) ADP can undergo further hydrolysis. What would you expect for the product of that reaction?

The monoanion of adenosine monophosphate (AMP) is an intermediate in phosphate metabolism: where \(\mathrm{A}=\) adenosine. If the \(\mathrm{p} K_{a}\) for this anion is \(7.21\), what is the ratio of \(\left[\mathrm{AMP}-\mathrm{OH}^{-}\right]\) to \(\left[\mathrm{AMP}-\mathrm{O}^{2-}\right]\) in blood at \(\mathrm{pH} 7.4\) ?