Concept explainers
Interpretation:
The sequence of the peptide consisting of 14 amino acids should be determined.
Concept introduction:
Trypsin cleaves peptide chains at the carboxyl side of the amino acids lysine (K) or arginine (R) if they are not followed by proline. Carboxypeptidase hydrolyzes the first peptide bond at the C-terminal of the peptide chain except for arginine (R), lysine (K) or proline (P). Chymotrypsin cleaves the peptide bond at the C-terminal where there ishydrophobic amino acids like tyrosine (Y), tryptophan (W), phenylalanine (F), leucine (L) and methionine (M). Cyanogen bromide hydrolyzes peptide bond at C-terminal of methionine residues. Homoserine is a product of cyanogen bromide cleavage by degradation of methionine.
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Chapter 3 Solutions
Biochemistry
- a. Suppose that the R group of a histidine residue in a protein in its native tertiary structure is buried in the interior of the protein and is involved in a salt bridge (ionic interaction) with an oppositely charged residue. Unfolding the protein exposes both of the charged groups to water. Would you expect the pKa of the His R group (side chain) in the native protein to be a) higher or b) lower than the pKa of the same residue in the unfolded protein? Why? b. Is the exocyclic NH2 in cytosine acidic or basic? Why? NH, `N'arrow_forwardA protein of unknown structure has been purified. Size-exclusion chromatography reveals that the native protein has a MW of 240,000. Chromatography in the presence of 6 M guanidine hydrochloride yields a single peak corresponding to a protein of MW 60,000. Chromatography in the presence of 6 M guanidine hydrochloride and 10 mM B-mercaptoethanol yields peaks for proteins of MW 34,000 and 26,000. Explain what can be determined about the structure of this protein from these data.arrow_forwardChymotrypsin digestion, separation of peptides, and Edmann technique give the sequences for peptide fragments as follows: C-1 G-A-E-A-T-E C-2 G-K-V-G-A-H-A-G-E-Y C-3 V-L-S-P-A-K-T-N-V-K-A-A-W What is the sequence for the peptide? NOTE: Label the fragments when reconstructing the peptide chain e.g. for trypsin T-1, T-2 etc...arrow_forward
- The sequence of a 29 aa long peptide can be determined from the following data: Treatment of the peptide with dansyl chloride reveals that the amino-terminal is Val. Trypsin digestion, separation of peptides, and Edmann technique give the sequences for peptide fragments as follows: T-1 V-G-A-H-A-G-E-Y-G-A-E-A-T-E T-2 A-A-W-G-KT-3 V-L-S-P-A-K T-4 T-N-V-Karrow_forwardConsider a protein in which a negatively charged glutamic acid side chain (pKa=4.2)(pKa=4.2) makes a salt bridge (ion-ion interaction) with a positively charged histidine side chain (pKa=6.5)(pKa=6.5).arrow_forwardA protein has been sequenced after cleavage of disulfide bonds. The protein is known to contain 3 Cys residues, located as shown here. Only one of the Cys has a free —SH group, and the other two are involved in an —S—S— bond. The only methionine and the only aromatic amino acid (Phe) in this protein are in the positions indicated. Cleavage of the intact protein (i.e., withdisulfide bonds intact) by either cyanogen bromide or chymotrypsin does not break the protein into two peptides. Where is the —S—S— bond (i.e., AB, BC, or AC)?arrow_forward
- Determine the sequence of the following 10-mer of ferritin using the data below. i. Complete acid hydrolysis of the 10-mer results in identification of 1A, 1D, 1E, 1F, 1H, 1K, 2L, 1T, 1Y ii. Digestion of the 10-mer with chymotrypsin results in 3 fragments containing (D, H, K, T), (F, L) and (A, E, L, Y) iii. Digestion of the 10-mer with V8 protease, which cuts on the C-side of acidic amino acids, results in three fragments containing (D, F, L, Y), (A, E, L) and (H, K, T) iv. Digestion with trypsin results in a fragment H-T and a fragment with all the other amino acids v. Treatment of the 10-mer with FDNB followed by complete acid hydrolysis results in the following two derivatives, DNP-1 and DNP-2 vi. Treatment of the 10-mer with a carboxypeptidase results in a free threoninearrow_forward11. Below is a folding energy funnel describing folding energy landscape of a protein. The width of the funnel indicates the entropy of the protein, and the height corresponds to the free energy. A) If A is the native fold structure, which state is a molten globule? How does this state differ from A in term of structures. B) Does this protein have multiple folding pathways or just one? C) which state has the lowest free energy? D) According to the width of the funnel, the native state B of the protein has the lowest entropy. If the protein fold A spontaneously to this state, does it violate the 2nd law of thermodynamics? Why or why not? (Hint: in the folding funnel, only the entropy of the protein alone is considered). E) Does the native state also have the lowest enthalpy. What makes the enthalpy decrease as the protein folds? 12. List four methods by which a protein can be denatured and briefly describe how these methods act to disrupt protein structure.arrow_forwardA/B: 3. Amino acid residues and peptide bonds (a) Draw the chemical structure of F, S and H joined by peptide bonds and also connected to neighboring residues as found in a protein. (b) Include all charges as expected at physiological pH (pH = 7.5) () Rank these three amino acid residues by hydrophobicity, pKa, and by nucleophilicity (d) For the central amino acid residue, identify the phi and psi dihedral angles by drawing a curved arrow indicating rotation about the chemical bond. (e) What group(s) eclipse each other if Phi = 0 degrees? Words and Pictures. (f) While Phi = 0 is not well tolerated, Psi = 0 is not uncommon, a so-called “allowed" but not most-favored region of the Ramachandran plot. What group(s) eclipse each other if Psi = 0 degrees and why is this less problematic than the situation created by Phi = 0. Words and Pictures H₂N* Pka: 9.13 H₂C с C._hydrophobicity: 1. phenylalanine (most) 2. Serine 3. Histidinelleast) ده H H. HIN OH I CH₂ CHO pka: 1. Serine (nighest) 2.…arrow_forward
- 1. What are the effects of a) amino acid composition and sequence and b) intramolecular and intermolecular forces of attraction to protein folding? 2. What molecular property of amino acids can be used to justity the concept that the "molecular part of the protein can exhibit the same property as the molecular 'whole' (protein molecule?). Provide a comprehensive discussion using one molecular property. 3. Discuss two metabolic disorders which are caused by protein misfolding. Explain the metabolic consequence of the disorder. 4. If a non-science person asks you what protein folding is and how the concept is related to metabolic disorders, how are you going to explain the concept? (please summarize the concepts used, thank you!)arrow_forwardDetermine the sequence of the decapeptide given the following information below. The decapeptide was hydrolyzed and confirmed to contain these amino acids: E, F, K, M, Q, S, T x 3, W Edman degradation product of the decapeptide: T trypsin fragments: a tetrapeptide (F,K,Q,T) and a hexapeptide (E,M,S,2T,W) chymotrypsin fragments: free S, a dipeptide (F,T) and a heptapeptide (E,K,M,Q,T,T,W) CNBr treatment of the heptapeptide (E,K,M,Q,T,T,W) yielded a tetrapeptide (K,T,M,Q) and a tripeptide (E,T,W) Edman degradation product of (E,T,W): E Use one-letter abbreviations only. One amino acid per blank.arrow_forwardPurification of a protein of unknown structure has been achieved. The natural protein has a molecular weight of 240,000, according to size-exclusion chromatography. Using a concentration of 6 M guanidine hydrochloride in the chromatography, a single peak can be identified as the molecular weight (MW) 60,000 of a protein. B-mercaptoethanol (BME) and guanidine hydrochloride (GHC) are used in tandem to produce proteins with mass masses of 34,000 and 26,000, respectively. The structure of this protein can be inferred from these facts.arrow_forward
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