Problem 1
Amino Acid Constituents of Glutathione Glutathione is an important peptide antioxidant found in cells from bacteria to humans. Identify the three amino acid constituents of glutathione. What is unusual about glutathione's structure?
Problem 4
Charge States of Alanine at Its \(\mathrm{pI}\) At a \(\mathrm{pH}\) equal to the isoelectric point (pI) of alanine, the net charge on alanine is zero. Two structures can be drawn that have a net charge of zero, but the predominant form of alanine at its \(\mathrm{pI}\) is zwitterionic. a. Why is alanine predominantly zwitterionic at its \(\mathrm{pI}\) ? b. What fraction of alanine is in the completely uncharged form at its \(\mathrm{pI}\) ?
Problem 7
Consider the structure of the amino acid isoleucine. a. How many chiral centers does isoleucine have? b. How many optical isomers does isoleucine have? c. Draw perspective formulas for all the optical isomers of isoleucine.
Problem 11
Mass Experimental results describing a protein's amino acid composition are useful to estimate the molecular weight of the entire protein. A quantitative amino acid analysis reveals that bovine cytochrome \(c\) contains \(2 \%\) cysteine \(\left(M_{\mathrm{r}} 121\right)\) by weight. a. Calculate the approximate molecular weight in daltons of bovine cytochrome \(c\) if the number of cysteine residues is 2 .
Problem 12
A protein has a molecular mass of \(400 \mathrm{kDa}\) when measured by size- exclusion chromatography. When subjected to gel electrophoresis in the presence of sodium dodecyl sulfate (SDS), the protein gives three bands with molecular masses of 180,160 , and 60 \(\mathrm{kDa}\). When electrophoresis is carried out in the presence of SDS and dithiothreitol, three bands again form, this time with molecular masses of 160, 90, and \(60 \mathrm{kDa}\). How many subunits does the protein have, and what is the molecular mass of each?
Problem 14
Histones are proteins found in eukaryotic cell nuclei, tightly bound to DNA, which has many phosphate groups. The pI of histones is very high, about 10.8. What amino acid residues must be present in relatively large numbers in histones? In what way do these residues contribute to the strong binding of histones to DNA?
Problem 15
One method for separating polypeptides makes use of their different solubilities. The solubility of large polypeptides in water depends on the relative polarity of their R groups, particularly on the number of ionized groups: the more ionized groups there are, the more soluble the polypeptides are. Which of each pair of polypeptides is more soluble at the indicated \(\mathrm{pH}\) ? a. (Gly) \(_{20}\) or (Glu) \(_{20}\) at pH \(7.0\) b. (Lys- Val) 3 or (Phe-Cys) \(_{3}\) at pH \(7.0\) c. (Ala-Ser-Gly) \(_{5}\) or (Asn-Ser-His) \(_{5}\) at \(\mathrm{pH} 6.0\) d. \((\mathrm{Ala}-\mathrm{Asp}-\mathrm{Phe})_{5}\) or \((\mathrm{Asn}-\mathrm{Ser}-\mathrm{His})_{5}\) at \(\mathrm{pH} 3.0\)
Problem 17
A purified protein is in a Hepes ( \(N\)-(2-hydroxyethyl)piperazine- \(N^{\prime}\)-(2-ethanesulfonic acid)) buffer at pH 7 with \(500 \mathrm{~mm} \mathrm{NaCl}\). A dialysis membrane tube holds a \(1 \mathrm{~mL}\) sample of the protein solution. The sample in the dialysis membrane floats in a beaker containing \(1 \mathrm{~L}\) of the same Hepes buffer, but with \(0 \mathrm{~mm} \mathrm{NaCl}\), for dialysis. Small molecules and ions (such as \(\mathrm{Na}^{+}, \mathrm{Cl}^{-}\), and Hepes) can diffuse across the dialysis membrane, but the protein cannot. a. Calculate the concentration of \(\mathrm{NaCl}\) in the protein sample, once the dialysis has come to equilibrium. Assume that no volume changes occur in the sample during the dialysis. b. Calculate the final \(\mathrm{NaCl}\) concentration in the protein sample after dialysis in \(250 \mathrm{~mL}\) of the same Hepes buffer, with \(0 \mathrm{~mm} \mathrm{NaCl}\), twice in succession.
Problem 18
Suppose a column is filled with a cation-exchange resin at \(\mathrm{pH}\) 7.0. In what order would the given peptides elute from the column if each has the same number of residues? Peptide A: Ala \(30 \%\), Asp \(10 \%\), Lys \(10 \%\), Ser \(15 \%\), Pro \(25 \%\), Cys \(10 \%\) Peptide B: Ile \(25 \%\), Asp \(20 \%\), Arg \(5 \%\), Tyr \(15 \%\), His \(5 \%\), Thr \(30 \%\) Peptide C: Ala \(40 \%\), Glu 5\%, Arg 20\%, Ser 5\%, His 5\%, Trp \(25 \%\)
Problem 21
Investigators purify a protein produced by yeast grown under standard growth conditions. They incubate the protein with trypsin and sequence the peptides produced using mass spectrometry. One of the detected peptides, called peptide X, has the sequence Ala-Ser-Ala-Gly-Lys-Glu-Leu-Ile-Phe- Gln. The investigators then isolate the same protein, but this time from yeast grown under the stress of ultraviolet irradiation. When the sample is analyzed, a peptide with the mass of peptide \(X\) is no longer found. Instead, detection reveals a new peptide with the same sequence, except for an amino acid that replaces Ser and has a molecular mass of 167 Da. The investigators conclude that the protein has been altered in response to stress, and that the serine residue in the analyzed peptide has been modified. An unmodified series residue has a molecular mass of \(87 \mathrm{Da}\). What modification might account for the change in the peptide's mass?
