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medical sciences
biochemistry
Fundamentals of biochemistry Life at the Molecular Level 4th edition Donald Voet, Judith G. Voet, Charlotte W. Pratt - Solutions
Is a protein as good a cellular buffer at physiological pH as its constituent amino acids would be if they were present as free amino acids in proportional concentrations in the cell? Explain.
Based on your rationale in the previous question, describe the difference in the dissociation constants of the α-COOH of GABA and glutamate, and the differences in the dissociation constants of the amino group in each of these amino acids.
100 mg of anhydrous powder of lysine is not completely soluble in 10 mL of water but dissolves completely when base is added. Explain.
Examine the amino acids below. Assume that the pK of the carboxyl group attached to the α carbon is 2.0 and that of the primary amine attached to the α carbon is 9.5 The pK's of ionizable R groups are shown below each structure. (a) Categorize these amino acids as nonpolar, uncharged polar, or
Shown below is a titration curve for glutamic acid. Draw the structure of the species that predominates at each labeled point.
Draw Fischer projections of L-aspartate and L-cysteine and show why L-Asp is (S)-Asp and L-Cys is (R)-Cys.
From which of the standard amino acids are the following physiologically active amines derived? What modifications gave rise to these products? (a) GABA (b) Histamine (c) Thyroxine (d) Dopamine
Study the functional groups of the amino acids in Table 4-1 and devise a Venn diagram showing amino acids in the following categories: nonpolar, polar, negatively charged, positively charged, aliphatic, small R groups, and bulky R groups. In a Venn diagram, objects with a given common property are
Circle the functional groups that are eliminated in the formation of a peptide bond between the amino acids shown below. Draw the structure of the dipeptide.
What percentage of the histidine imidazole group is protonated at pH 7.2?
What percentage of the cysteine sulfhydryl group is deprotonated at pH 7.6?
In proteins, the imidazole groups of histidine play key roles in catalysis involving reversible protonation/deprotonation events. The pK of the imidazole group is influenced by surrounding amino acids and in many enzymes is near 7. (a) What is the significance of this apparent pK in catalysis? (b)
(a) What is the net charge at neutral pH of a tripeptide containing only alanine? (b) How does the total number of negative and positive charges change following hydrolysis of the tripeptide?
(a) + 1; (b) 0; (c) - 1; (d) - 2
(a) 2; (b) 1; (c) 0; (d) - 1.
Calculate the pI of (a) Ala, (b) His, and (c) Glu.
Estimate the isoelectric point of a Ser-His dipeptide. Explain why this value is only an estimate.
Draw the peptide ATLDAK. (a) Calculate its approximate pI. (b) What is its net charge at pH 7.0?
The protein insulin consists of two polypeptides termed the A and B chains. Insulins from different organisms have been isolated and sequenced. Human and duck insulins have the same amino acid sequence with the exception of six amino acid residues, as shown below. Is the pI of human insulin lower
Indicate whether the following familiar objects are chiral or nonchiral: (a) A glove; (b) A tennis ball; (c) A screw; (d) This page; (e) A snowflake; (f) A spiral staircase; and (g) A shoe.
Circle the chiral carbons in the following compounds:
Draw the four stereoisomers of threonine.
The two CαH atoms of Gly are said to be prochiral, because when one of them is replaced by another group, Cα becomes chiral. Draw a Fischer projection of Gly and indicate which H must be replaced with CH3 to yield D-Ala.
The bacterially produced antibiotic gramicidin A forms channels in cell membranes that allow the free diffusion of Na and K ions, thereby killing the cell. This peptide consists of a sequence of D- and L-amino acids. The sequence of a segment of five amino acids in gramicidin A is
Draw the structure of Lys and Ala linked by an isopeptide bond.
Taurine (2-aminoethanesulfonic acid) is sometimes called an amino acid.(a) Explain why this designation is not valid. (b) From which of the 20 standard amino acids is taurine derived? Describe the chemical change(s) that occurred. 5. Draw the dipeptide Asp-His at pH
Draw the dipeptide Asp-His at pH 7.0.
A sample of the amino acid tyrosine is barely soluble in water. Would a polypeptide containing only Tyr residues, poly(Tyr), be more or less soluble, assuming the total number of Tyr groups remains constant?
Discuss the disadvantages of each of the following in the handling of proteins: (a) Low concentrations of protein
When immunoaffinity chromatography is used to purify a protein, the cell lysate is often subjected to one or more purification steps before the material is applied to the immunoaffinity column. Why is this necessary?
Describe two methods for determining the molecular mass of a polypeptide. Which is more accurate and why?
Shown below are the biochemical fractionation and purification of an enzyme. Fill in the table on the next page with the values for specific activity and fold purification, and answer the accompanying questions.(a) Which step provides the greatest purification?(b) Is the enzyme pure? How can purity
Match the terms below with the accompanying statements. (More than one term may apply to a statement.) A. Dansyl chloride D. 2-mercaptoethanol B. Phenylisothiocyanate E. Cyanogen bromide C. Iodoacetate _____ An alkylating agent that reacts with Cys residues. _____ A reducing agent that carries out
How many fragments can be obtained by treating bovine insulin with endopeptidase V8? Does this number depend on whether the protein is first reduced and alkylated?
You have a protein whose molecular mass is about 6.8 kD according to SDS-PAGE. However, SDS-PAGE of the protein in the presence of 2-mercaptoethanol reveals two bands of 2.3 kD and 4.5 kD. Are these polypeptides too large for direct sequencing by an automated sequencer using Edman degradation? What
You have a polypeptide that has been degraded with cyanogen bromide and trypsin. The sequences of the fragments are listed below (using one-letter codes). Is there enough information to derive the complete amino acid sequence of the polypeptide? What further treatments might support the deduced
You want to know the amino acid sequence of a purified polypeptide (1341 D). Your new technician has performed the analyses outlined below. Do you have enough data to determine the amino acid sequence? (a) Partial acid hydrolysis yields tripeptides with the following amino acid sequences as
Compare the molecular mass (M) of horse heart apomyoglobin calculated from the two adjacent peaks at 1884.7 and 1696.3, and 893.3 and 848.7 (Figure 5-16b). How do these results compare with those in Sample Calculation 5-1?
Explain why single-nucleotide mutations in DNA occur at a constant rate, but the rate of protein evolution varies.
List possible ways to track the presence of a protein during its purification.
Rank the following residue positions in cytochrome c in order from least to most conserved: 56, 61, 74, 85, and 89.
Which protein(s) shown in Figure would be most useful for assessing the phylogenetic relationships between mammalian species)? Explain.
The sequences of two cAMP regulatory transcription factors were compared using the BLAST alignment program from NCBI. The results below show the sequences from Escherichia coli (the Query sequence) and Methylobacterium extorquens (the Sbjct sequence). The BLAST "hit" compares residues 190-369 of
Comparisons between amino acid sequences can be used to understand which areas of a polypeptide are important for its function. A large family of proteins in bacteria includes a transcriptional regulator called the cAMP regulatory or activator protein (CRP or CAP). (i) Go to the NCBI site at
You have several cell lysates and want to determine which of them contain protein X in its phosphorylated form (with phosphorylation occurring on a tyrosine residue). You have two antibodies: One recognizes phosphotyrosine and the other recognizes protein X. Describe how you would analyze the cell
The salting out procedure outlined in Fig. 5-5 results in significant protein purification by eliminating many less- and more-soluble proteins. What is its other advantage?
You wish to separate two proteins in solution by selectively precipitating one of them. What method could you use other than salting out?
Evaluate the solubility of the following peptides at the given pH. For each pair, which peptide is more soluble and why? (a) pH 7: Gly20 and (Glu-Asp)10 (b) pH 5: (Cys-Ser-Ala)5 and (Pro-Ile-Leu)5 (c) pH 7: Leu3 and Leu10
Would you use an anion or cation exchange column to purify bovine histone at pH 7.0?
The protein contains two 60-kD polypeptides and two 40-kD polypeptides. Each 40-kD chain is disulfide bonded to a 60-kD chain. The 100-kD units associate noncovalently to form a protein with a molecular mass of 200 kD.
Because protein 1 has a greater proportion of hydrophobic residues (Ala, Ile, Pro, Val) than do proteins 2 and 3, hydrophobic interaction chromatography could be used to isolate it.
(a)(b)
A protein has an apparent mass of 800 kD by gel filtration chromatography, but SDS-PAGE shows a single band at a position corresponding to 200 kD. In an ultracentrifuge, will the protein exhibit a sedimentation coefficient corresponding to 200 kD or 800 kD?
Purification of Myoglobin (Mb). Purification tables are often used to keep track of the yield and purification of a protein. The specific activity is a ratio of the amount of the protein of interest, in this case Mb, obtained at a given step (mol or enzyme units) divided by the amount (mg) of
A 50-mL crude extract of skeletal muscle contains 32 mg of protein per mL. TenL of the extract catalyzes a reaction at a rate of 0.14 μmol product formed per minute. The extract was fractionated by ammonium sulfate precipitation, and the fraction precipitating between 20% and 40% saturation was
If insulin were treated with mercaptoethanol to break its disulfide bonds, and then the mercaptoethanol were removed so that disulfide bonds could re-form, how many different ways could the two polypeptide chains become linked to each other (assuming that one or two disulfide bonds can form between
You wish to determine the sequence of a polypeptide that has the following amino acid composition.(a) What is the maximum number of peptides you can expect if you cleave the polypeptide with cyanogen bromide? (b) What is the maximum number of peptides you can expect if you cleave the polypeptide
Electrospray ionization mass spectrometry (ESI-MS) of proteins involves creating positively charged ions of the protein and separating them according to their mass-to-charge ratio (mz).(a) What causes the different positive charges on different particles of the protein?(b) The amino acid
(a) The ESI-MS spectrum below was obtained for HEWL. Using peaks 5 and 6, calculate the molecular mass of HEWL (see Sample Calculation 5-1).[Spectrum obtained from www.astbury.leeds.ac.uk/facil/MStut/mstutorial.htm] (b) What is the charge on the ion that makes peak 5?
Treatment of a polypeptide with 2-mercaptoethanol yields two polypeptides: 1. Ala-Val-Cys-Arg-Thr-Gly-Cys-Lys-Asn-Phe-Leu 2. Tyr-Lys-Cys-Phe-Arg-His-Thr-Lys-Cys-Ser Treatment of the intact polypeptide with trypsin yields fragments with the following amino acid compositions: 3. (Ala, Arg, Cys2, Ser,
You wish to sequence the light chain of a protease inhibitor from the Brassica nigra plant. Cleavage of the light chain by trypsin and chymotrypsin yields the following fragments. What is the sequence of the light chain? Chymotrypsin 1. Leu-His-Lys-Gln-Ala-Asn-Gln-Ser-Gly-Gly-Gly- Pro-Ser 2.
In site-directed mutagenesis experiments, Gly is often successfully substituted for Val, but Val can rarely substitute for Gly. Explain.
Below is a list of the first 10 residues of the B helix in myoglobin from different organisms. Position 1 2 3 4Based on this information, which positions (a) appear unable to tolerate substitutions, (b) can tolerate conservative substitution, and (c) are highly variable?
Sketch a phylogenetic tree for the family of homologous proteins whose partial sequences are given below.
Draw a different phylogenetic tree based on the data in Problem 29.In Problem 29
You are trying to purify a protein that is soluble in a solution of 2 M ammonium sulfate. After centrifugation to remove other proteins that have precipitated at this high salt concentration, you recover the supernatant to assay the target protein's activity in a cell culture system. (a) Explain
Explain how you could use a column containing carboxymethyl groups to separate serum albumin and ribonuclease A.
Explain why a certain protein has an apparent molecular mass of 90 kD when determined by gel filtration and 60 kD when determined by SDS-PAGE in the presence or absence of 2-mercaptoethanol.Which molecular mass determination is more accurate?
Why does the peptide bond result in a planar configuration for its adjoining functional groups?
What is the repeating sequence of collagen and how is it essential to the structure of the triple coils of collagen fibers?
Organic compounds containing radioactive atoms can be used to follow the biosynthesis of molecules in cells and organisms. In these experiments, the amount of radioisotope in proteins derived from the cells or organisms is monitored. The administration of 14C-labeled 4-hydroxyproline to mice
List the three amino acids that are least likely to occur in a β sheet.
Examine Table 4-1 (pp. 76-77) and determine which amino acids might exhibit identical electron densities at 2.0-Å resolution.
What advantages does NMR provide over X-ray crystallography in characterizing protein structure? What is the major limitation of NMR analysis?
What specific role does knowledge of the primary amino acid sequence play in the determination of tertiary structure by X-ray crystallography?
How does the polarity or charge of an amino acid affect its likely location within a protein?
How does the ratio of hydrophilic to hydrophobic amino acid residues change in a series of globular proteins ranging from 10 to 50 kD?
In the dipeptide below, indicate which bonds are described by φ and ψ.
Go to the National Center for Biotechnology Information (NCBI: www.ncbi.nlm.nih.gov/) and click on the word Structure along the menu line (last word on the right). If you choose to download the Cn3D program, you will be able to view the three-dimensional structures directly from the links after you
The subunit composition of an oligomeric protein can be determined by treating the protein with a cross-linking agent (a bifunctional molecule that reacts with and links groups in two different portions of the polypeptide), denaturing the protein, and analyzing the products by SDS-PAGE (Section
Consider the equilibrium of an oligomer:2 MONOMERS ‡† DIMERThe ΔH° for this reaction is positive and varies little between 4°C and 45°C. TΔS°, in contrast, varies widely over the same temperature range. The behaviors of ΔH° and
What thermodynamic consideration prevents ion pairs from contributing significantly to protein stability?
What is the probability of recovering the native conformation (as judged by biological activity) of a dimeric protein, each of whose subunits contains three disulfide bonds? Assume that the disulfide linkages form randomly.
Calculate the maximum length of a polypeptide that could recover its native conformation in about one day if the polypeptide explored all possible conformations.
To appreciate the role of hierarchical assembly in the rapid renaturation of proteins, consider the equation t = 10n/1013 as a reasonable approximation of renaturation time for a globular protein in which n represents the number of nucleating structures (α helices and β sheets). How does this
Shown below is a portion of poly-β-alanine10. Comment on the secondary structure of this peptide.
Assume that the average molecular mass of an amino acid is 112, and that 4 ATP equivalents are expended to form a peptide bond. Using the current model for protein folding in GroEL/ES, compare the cost of protein synthesis with the cost of protein folding for a 70-kD polypeptide in E. coli.
What statement(s) in the text suggests that native protein structure is highly labile?
How do R groups constrain the potential conformations of a protein?
Study Figure and describe the orientation of the groups that contribute to the dipole moment of the α helix and the overall direction of this dipole moment.
How does the 7-residue repeat of α keratin promote formation of a coiled coil?
Wool from sheep is steamed to generate long fibers for knitting. Wool sweaters shrink after subsequent drying with heat. Explain what is happening at the molecular level.
Draw a cis peptide bond and identify the groups that experience steric interference.
Explain why gelatin, which is mostly collagen, is nutritionally inferior to other types of protein.
Globular proteins are typically constructed from several layers of secondary structure, with a hydrophobic core and a hydrophilic surface. Is this true for a fibrous protein such as α keratin?
Which of the following polypeptides is most likely to form an α helix? (a) CRAGNRKIVLETY (b) SEDNFGAPKSILW (c) QKASVEMAVRNSG
The X-ray crystallographic analysis of a protein often fails to reveal the positions of the first few and/or the last few residues of a polypeptide chain. Explain.
You are performing site-directed mutagenesis to test predictions about which residues are essential for a protein's function. Which of each pair of amino acid substitutions listed below would you expect to disrupt protein structure the most? Explain. (a) Val replaced by Ala or Phe. (b) Lys replaced
Laboratory techniques for randomly linking together amino acids typically generate an insoluble polypeptide, yet a naturally occurring polypeptide of the same length is usually soluble. Explain.
Under physiological conditions, polylysine assumes a random coil conformation. Under what conditions might it form an α helix?
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