Chapter 28

Refer to a typical Escherichia coli bacterium. This is a cylindrical cell about \(2 \mu\) m long and \(1 \mu\)m in diameter, weighing about \(2 \times 10^{-12}\)g and containing about \(80 \%\) water by volume. The intracellular \(\mathrm{pH}\) is 6.4 and \(\left[\mathrm{K}^{+}\right]=1.5 \times 10^{-4} \mathrm{M}\) Determine the number of (a) \(\mathrm{H}_{3} \mathrm{O}^{+}\) ions and (b) \(\mathrm{K}^{+}\) ions in a typical cell.

Refer to a typical Escherichia coli bacterium. This is a cylindrical cell about \(2 \mu\) m long and \(1 \mu\)m in diameter, weighing about \(2 \times 10^{-12}\)g and containing about \(80 \%\) water by volume. Calculate the number of lipid molecules present, assuming their average molecular mass to be 700 u and the lipid content to be \(2 \%\) by mass.

Refer to a typical Escherichia coli bacterium. This is a cylindrical cell about \(2 \mu\) m long and \(1 \mu\)m in diameter, weighing about \(2 \times 10^{-12}\)g and containing about \(80 \%\) water by volume. The cell is about \(15 \%\) protein by mass with \(90 \%\) of the protein in the cytoplasm. Assuming an average molecular mass of \(3 \times 10^{4}\) u, how many protein molecules are present in the cytoplasm?

Refer to a typical Escherichia coli bacterium. This is a cylindrical cell about \(2 \mu\) m long and \(1 \mu\)m in diameter, weighing about \(2 \times 10^{-12}\)g and containing about \(80 \%\) water by volume. A single chromosomal DNA molecule contains about 4.5 million nucleotide units. If this molecule were extended so that the nucleotide units were \(450 \mathrm{pm}\) apart, what would be the length of the molecule? How does this compare with the length of the cell itself? What does this result suggest about the shape of the DNA molecule?

Write structural formulas for the following. (a) glyceryl palmitolauroeleostearate (b) tripalmitin (c) potassium myristate (d) butyl oleate

Describe the similarities and differences between (a) trilaurin and trilinolein, (b) a soap and a phospholipid such as a lecithin.

Write a structural formula for a generic phosphatidic acid-an acid that produces a cephalin when esterified with ethanolamine and a lecithin when esterified with choline. Mono- and diglycerides are found in many processed foods. Write structural formulas for a generic monoglyceride and a generic diglyceride.

Oleic acid is a moderately unsaturated fatty acid. Linoleic acid is polyunsaturated. What structural feature characterizes polyunsaturated fatty acids? Is stearic acid polyunsaturated? Is eleostearic acid? Why do you suppose safflower oil is so highly recommended in dietary programs?

Write structural formulas to represent the products of the saponification of tripalmitin with \(\mathrm{NaOH}(\mathrm{aq})\).

Write the structure for the straight-chain form of L-glucose. Does the structure determine if this isomer is levorotatory? Explain.

Describe the similarities and differences in the structures of the following three compounds. (a) \(\beta-\mathrm{D}-(+)-\) glucose; (b) \(\mathrm{D}-(-)\) -arabinose; \((\mathrm{c}) \mathrm{D}-(+)-\mathrm{glucose}\) .

The following terms are all related to stereoisomers and their optical activity. Explain the meaning of each: (a) dextrorotatory; (b) levorotatory; (c) racemic mixture; (d) \((R)\).

The following terms are all related to optical isomers. Explain the meaning of each: (a) diastereomers; (b) enantiomers; (c) \((-) ;\) (d) D configuration.

The pure \(\alpha\) and \(\beta\) forms of \(\mathrm{D}\) -glucose rotate the plane of polarized light to the right by \(112^{\circ}\) and \(18.7^{\circ},\) respectively (denoted as +112 and +18.7 ). Are these two forms of glucose enantiomers or diastereomers?

Describe what is meant by each of the following terms, using specific examples where appropriate: (a) \(\alpha\) -amino acid; (b) zwitterion; (c) isoelectric point; (d) peptide bond; (e) tertiary structure.

Describe what is meant by each of the following terms, using specific examples where appropriate: (a) polypeptide; (b) protein; (c) N-terminal amino acid; (d) \(\alpha\) helix; (e) denaturation.

Write the formulas of the species expected if the amino acid phenylalanine is maintained in (a) \(1.0 \mathrm{M}\) HCl; (b) \(1.0 \mathrm{M} \mathrm{NaOH} ;\) (c) a buffer solution with \(\mathrm{pH}=5.7\).

Draw plausible structures for the amino acid histidine at (a) \(\mathrm{pH}=3.0 ;\) (b) \(\mathrm{pH}=7.6 ;\) (c) \(\mathrm{pH}=12.0\).

Write the structures of (a) alanylcysteine; (b) threonylvalylglycine.

For the polypeptide Met-Val-Thr-Cys, (a) write the structural formula; (b) name the polypeptide. [Hint: Which is the N-terminal, and which is the C-terminal amino acid?]

Draw condensed structural formulas showing what form you would expect for the essential amino acid threonine (a) in strongly acidic solutions; (b) at the isoelectric point; and (c) in strongly basic solutions.

Draw condensed structural formulas for the following amino acids buffered at \(\mathrm{pH}\) 6.0: (a) aspartic acid; (b) lysine; and (c) alanine.

Write the structures of (a) the different tripeptides that can be obtained from a combination of alanine, serine, and lysine; (b) the tetrapeptides containing two serine and two alanine amino acid units.

Write the structures of the different tetrapeptides that can be obtained from a combination of alanine, lysine, serine, and phenylalanine. Give the abbreviated formula of each (such as Ala-Lys-Ser-Phe), starting at the N-terminal end.

After undergoing complete hydrolysis, a polypeptide yields the following amino acids: Gly, Leu, Ala, Val, Ser, Thr. Partial hydrolysis yields the following fragments: Ser-Gly-Val, Thr-Val, Ala-Ser, Leu-Thr-Val, Gly-Val-Thr. An experiment using a marker establishes that Ala is the N-terminal amino acid. (a) Establish the amino acid sequence in this polypeptide. (b) What is the name of the polypeptide?

After undergoing complete hydrolysis, a polypeptide yields the following amino acids: Ala, Gly, Lys, Ser, Phe. Partial hydrolysis yields the following fragments: Ala-Lys-Ser, Gly-Phe-Gly, Ser-Gly, Gly-Phe, Lys-Ser-Gly. An experiment using a marker establishes that Ala is the N-terminal amino acid. (a) Establish the amino acid sequence in this polypeptide. (b) What is the name of the polypeptide?

Describe what is meant by the primary, secondary, and tertiary structure of a protein. What is the quaternary structure? Do all proteins have a quaternary structure? Explain.

Sickle-cell anemia is sometimes referred to as a "molecular" disease. Comment on the appropriateness of this term.

The amino acid ( \(R\) )-alanine is found in insect larvae. Draw the Fischer projection of this amino acid.

The amino acid ( \(R\) )-serine is foEven number of switches causes no change in the configurationund in earthworms. Draw the Fischer projection of this amino acid.

Draw the dashed-wedged line structure for ( \(S\) )-alanine and (S)-phenylalanine.

Draw the dashed-wedged line structure for ( \(R\) )-proline and (S)-valine.

What are the two major types of nucleic acids? List their principal components.

DNA has been called the "thread of life." Comment on the appropriateness of this expression.

If one strand of a DNA molecule has the base sequence of \(\mathrm{AGC}\), what must be the sequence on the opposite strand? Draw a structure of this portion of the double helix, showing all hydrogen bonds.

If one strand of a DNA molecule has the base sequence TCT, what must be the sequence on the opposite strand? Draw a structure of this portion of the double helix, showing all hydrogen bonds.

The term "epimer" is used to describe diastereomers that differ in the configuration about a single carbon atom. Which pairs of the eight possible aldopentoses are epimers?

Bradykinin is a nonapeptide obtained by the partial hydrolysis of blood serum protein. It causes a lowering of blood pressure and an increase in capillary permeability. Complete hydrolysis of bradykinin yields three proline (Pro), two arginine (Arg), two phenylalanine (Phe), one glycine (Gly), and one serine (Ser) amino acid units. The N-terminal and C-terminal units are both arginine (Arg). In a hypothetical experiment, partial hydrolysis and sequence proof reveals the following fragments: Gly-Phe-Ser-Pro; Pro-Phe-Arg; Ser-Pro-Phe; Pro-Pro-Gly; Pro-Gly-Phe; Arg-Pro-Pro; Phe-Arg. Deduce the sequence of amino acid units in bradykinin.

Projection formulas impose certain limitations and care must be taken in drawing and manipulating them. Use (R)-(+)-glyceraldehyde as an example and show that: (a) Rotating the Fischer projection by \(90^{\circ}\) in the plane of the paper produces the opposite absolute configuration. What is the effect of rotation by \(180^{\circ}\) and \(270^{\circ}\) in the plane of the paper? (b) Interchanging two substituents converts one enantiomer into the other. What is the effect of two such interchanges?

Eighteen of the nineteen 1 -amino acids have the \(S\) configuration at the \(\alpha\) carbon (the first carbon after the carboxyl carbon). Cysteine is the only 1 -amino acid that has an \(R\) configuration. Explain.

The systematic (IUPAC) name for the amino acid threonine is \((2 S, 3 R)-2\) -amino- 3 -hydroxybutanoic acid. The systematic name indicates that threonine has two stereocenters, at positions 2 and \(3,\) with \(S\) and \(R\) configurations, respectively. Draw the Fischer projection of threonine. How many other possible stereoisomers of threonine are there?

Coupling ATP hydrolysis to a thermodynamically unfavorable reaction can shift the equilibrium of a reaction (see Chapter 19). (a) Calculate \(K\) for the hypothetical reaction \(A \longrightarrow B\) when \(\Delta G^{\circ}\) is \(23 \mathrm{kJ} \mathrm{mol}^{-1}\) at \(25^{\circ} \mathrm{C}\) (b) Calculate \(K\) for the same reaction when it is coupled to the hydrolysis of \(\operatorname{ATP}\left(\Delta G^{\circ \prime}=-30 \mathrm{kJ} \mathrm{mol}^{-1}\right)\) Compare with the value obtained in part (a). (c) Many cells maintain [ATP] to [ADP] ratios of 400 or more. Calculate the ratio of \([\mathrm{B}]\) to \([\mathrm{A}]\) when \(\left.[\mathrm{ATP}] /[\mathrm{ADP}]=400 \text { and } \mathrm{P}_{\mathrm{i}}\right]=5 \mathrm{mM} .\) Compare this ratio to that for the uncoupled reaction.

The so-called Ruff degradation is a chain-shortening reaction in which an aldose chain is shortened by one C atom, hexoses, for example, being converted into pentoses. In the Ruff degradation, the calcium salt of an aldonic acid (the corresponding carboxylic acid of an aldose) is oxidized with hydrogen peroxide. Ferric ion catalyzes the reaction. The calcium salt of the aldonic acid necessary for the Ruff degradation is obtained by oxidizing an aldose with an aqueous solution of bromine and then adding calcium hydroxide. The reaction scheme is as follows where \(R\) represents the rest of the chain of the aldose. (a) Show that D-glucose can be degraded into D-arabinose. Which other aldose can be degraded into D-arabinose? (b) Which two monosaccharides can be degraded into D-glyceraldehyde by employing the Ruff degradation only once?

If \(\mathrm{D}-(+)\) -glyceraldehyde is treated with \(\mathrm{HCN}\) in aqueous solution under basic conditions for three days at room temperature, cyanohydrins are formed (see Chapter 27). The cyanohydrins are not isolated, but are hydrolyzed to hydroxyacids in the same reaction mixture using dilute sulfuric acid. In this process, a new stereocenter is formed in the molecule. The products are diastereomers, formed in unequal amounts, and separable from each other by recrystallization because of their different physical properties, including solubilities. The trihydroxybutanoic acids are separated and then oxidized to tartaric acid with dilute nitric acid, which oxidizes only the primary alcohol group. (a) Ignoring stereochemistry, draw the reaction sequence for the transformations described above and hence deduce the structure of tartaric acid. (b) Starting from the Fischer projection of \(\mathrm{D}-(+)-\) glyceraldehyde and using the reaction scheme from part (a), draw Fischer projections of the two trihydroxybutanoic acids formed and designate the chiral centers as \(R\) or \(S\). (c) Starting from the Fischer projection of \(\mathrm{D}-(+)-\) glyceraldehyde and using the reaction scheme from part (a), draw Fischer projections of the two forms of tartaric acid formed and designate the chiral centers as \(R\) or \(S\). (d) One form of tartaric acid obtained is optically active, rotating the plane of polarized light in a negative sense \((-) .\) The other isomer formed, called meso-tartaric acid, is not optically active. Explain why the other isomer is not optically active. Draw the dashed-wedged line structure that corresponds to the Fischer projection of meso-tartaric acid. Can you describe how the two halves of the molecule are related? Using Fischer projections, write equations for the conversion of \(L-(-)-\) glyceraldehyde to tartaric acid. Show clearly the stereochemistry of the tartaric acids that are formed, and indicate whether you expect them to be optically active.

In your own words, define the following terms or symbols: (a) \((+) ;\) (b) \(\mathrm{L} ;\) (c) sugar; (d) \(\alpha\) -amino acid; (e) isoelectric point.

Briefly describe each of the following ideas, phenomena, or methods: (a) saponification; (b) chiral carbon atom; (c) racemic mixture; (d) denaturation of a protein.

Explain the important distinctions between each pair of terms: (a) fat and oil; (b) enantiomer and diastereomer; (c) primary and secondary structure of a protein; (d) DNA and RNA; (e) ADP and ATP.

The substance glyceryl trilinoleate (linoleic acid: \(\left.\mathrm{C}_{17} \mathrm{H}_{31} \mathrm{COOH}\right)\) is best described as a (a) fat; (b) oil; (c) wax; (d) fatty acid; (e) phospholipid.

Of the following names, the one that refers to a simple sugar in its cyclic (ring) form is (a) \(\beta\) -galactose; (b) \(L-(-)\) -glyceraldehyde; (c) \(\mathrm{D}-(+)\) -glucose; (d) DL-erythrose; (e) \((R)-(+)\) -glyceraldehyde.

The coagulation of egg whites by boiling is an example of (a) saponification; (b) inversion of a sugar; (c) hydrolysis of a protein; (d) denaturation of a protein; (e) condensation of amino acids.