4. Gamma turns are divided into two classes based on the phi and psi rotationalbond angles of the residue at positions n + 1. In the classical gamma turn, theresidue at position n + 1 has phi = + 70 degrees and psi = -60 degrees, whereasin the inverse gamma turn, the residue at position n + 1 has phi = - 70 degreesand psi = + 60 degrees. Draw a Ramachandran plot and indicate the location ofthese bond angles on your plot.

An illustration of the permitted and forbidden areas of the phi and psi dihedral angles in the…

Answered: Gamma turns are divided into two…

Biochemistry

9th Edition

ISBN:9781319114671

Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Chapter1: Biochemistry: An Evolving Science

Section: Chapter Questions

Problem 1P

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2. Amino acid analysis of the a heptapeptide gave the following residues: Asp Glu Leu Lys Met Tyr Trp NH4+ The following facts were observed: a) Trypsin treatment had no effect. b) The phenylthiohydantoin released by Edman degradation was -C-CH₂ What is the amino acid sequence for this heptapeptide? OH c) Brief chymotrypsin treatment yielded several products including a dipeptide and a tetrapeptide. The tetrapeptide contained Glu, Leu, Lys and Met is some order. d) Cyanogen bromide treatment afforded a tetrapeptide that had a net positive charge at pH 7 and tripeptide that had a zero net charge at pH 7.
6 (a) A decapeptide has the following amino acid composition: Ala2 , Arg, Cys, Glu, Gly, Leu, Lys, Phe, Val Partial hydrolysis yields the following tripeptides: Cys-Glu-Leu + Gly-Arg-Cys + Leu-Ala-Ala+ Lys-Val-Phe + Val-Phe-Gly. Reaction of the decapeptide with 2,4-dinitrofluorobenzene yields 2,4-dinitrophenylysine. From the experimental data, deduce the primary structure of the decapeptide. (b) Suggest a scheme you will follow to synthesize the dipeptide Ala-Gly
5 25) Although the UV280 extinction coefficient of BSA is well known, why was the BCA assay employed to measure protein concentration of the folate labeled BSA? Please provide an explanation. (C) Would the use of reducing agents have an affect on the tertiary structure of BSA—please explain your answer (you will need to investigate the structure of BSA beyond this article)?
33. Gel filtration chromatography shows that the molecular weight of a protein is 240,000 Daltons. However, when the protein was subjected to SDS-PAGE in the absence of ß- mercaptoethanol, two polypeptides (100,000 Daltons, 140,000 Daltons) were identified. Furthermore, when the protein was subjected to SDS-PAGE in the presence of ß- mercaptoethanol, three polypeptides (100,000 Daltons, 90,000 Daltons, and 50,000 Daltons) were identified. Which of the following statements is true of the protein? A. The protein is composed of three polypeptides. B. The three-dimensional structure of the protein is stabilized by both covalent and non- covalent bonds. C. Both A and B. D. Neither A nor B. 34. What is purpose of SDS in SDS-PAGE? E. To selectively bind the target protein F. To maintain buffer pH in the gel G. To cause the separation of proteins to be on the basis of molecular weight only H. To initiate polymerization of acrylamide to form gel
7. Chalcone isomerase catalyzes the reaction illustrated below. A series of modification experiments were performed on this enzyme to identify which amino acid residues might be in the active site and which might promote the cyclization reaction. OH Ho. Но Explain the following results: A) Acetic anhydride treatment inhibited enzyme activity. B) Pyrocarbonate inhibited activity and was found to modify 7 residues. However, this enzyme only contains 6 His and modification of these did not affect activity. C) lodoacetate inhibited activity but this effect coult be decreased in the presence of substrate or product. D) Methane methanethiol sulfonate modified the enzyme but did not inhibit catalytic turnover. In addition, this modification was reversed in the presence of B-mercaptoethanol. keNyons Rengent
The enzyme creatine kinase catalyzes the ATP-dependent phosphorylation of creatine. Propose a mechanism for the reaction described using the curved arrow convention. Show the complete structure of the nucleotide.
2. 4. The sequence of a peptide A formed by 16 amino acids was determined using a combination of methods that included the use of the Sanger's reagent, protease treatment and SDSPAGE/2D-electropheresis. The following data was obtained from the mentioned experiments: (a) Treatment of peptide A with an excess of fluoro-2,4-dinitrobenzene followed by peptide digestion with concentrated HI and analysis of the hydrolysate showed the presence of 2,4-dinitroderivatives of Ala and Glu. (b)Treatment of the same peptide with carboxypeptidase A resulted in free Tyr and free Ala. (c) SDS-PAGE of peptide A showed only one band at a molar mass of 18 kDa. After treatment with ß-mercaptoethanol and a second electrophoresis trial, one band appeared on the gel but this time the molar mass of the band was approximately 900 Da. Isoelectric focusing of the peptide isolated from this band resulted in two separate bands at pl 9.8 and 4.5 (d) After treatment of peptide A with beta-mercaptoethanol and…
The melting curve for the polyribonucleotide poly(A) is shown below. (a) Explain why absorbance increases with increasing temperature. (b) Why does the shape of the curve differ from the one shown in Fig. ?
1. a. draw the L- & R- stereoisomer of the amino acid T using a fischer projection or a newman projection. b. draw the tripeptide LEM in the protonation state you would expect at physiological pH. show the position of phi and psi angles on the E residue
1. Choose the proper structure of the predominant form of L-M-L-P-D-T at pH 5. Provide a short explanation. 2. Choose the proper structure of the predominant form of L-A-L-Y at pH 11. Provide a short explanation.
VII. Analysis of a peptide antibiotic purified from a strain of Bacillus brevii resulted in the following significant information: Complete hydrolysis of the peptide yielded equimolar amounts of Leu, Orn, Phe, Pro, and Val Molecular weight of the peptide was estimated to be aroung 1,200 Da The peptide failed to undergo hydrolysis when treated with carboxypeptidase Partial hydrolysis and then chromatographic separation of products yielded the following di- and tripeptides: Leu-Phe, Phe-Pro, Orn-Leu, Val-Orn, Val-Orn-Leu, Phe-Pro-Val, Pro-Val-Orn Treament with dinitrofluorobenzene (DNFB) followed by complete hydrolysis yielded only free amino acids and the DNFB-derivatized ornithine at its side chain Using this set of information available to you, deduce the amino acid sequence of this peptide antibiotic. Write your final peptide sequence only using 3-letter abbreviations. /
1. Analysis of a peptide antibiotic purified from a strain of Bacillus brevii resulted in the following significant information: - Complete hydrolysis of the peptide yielded equimolar amounts of Leu, Orn, Phe, Pro, and Val - Molecular weight of the peptide was estimated to be aroung 1,200 Da - The peptide failed to undergo hydrolysis when treated with carboxypeptidase - Partial hydrolysis and then chromatographic separation of products yielded the following di- and tripeptides: Leu-Phe, Phe-Pro, Orn-Leu, Val-Orn, Val-Orn-Leu, Phe-Pro-Val, Pro-Val- - Orn Treament with dinitrofluorobenzene (DNFB) followed by complete hydrolysis yielded only free amino acids and the DNFB-derivatized ornithine at its side chain By using the above information, deduce the amino acid sequence of this peptide antibiotic. Write the final peptide sequence using 3-letter abbreviations. Show the complete and step by step solution.

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