1. Draw the tripeptide: Val-Leu-Met at pH 7 with the N-terminus to the left and C-terminus tothe right. On your drawing, do the following:a. Draw a triangle around the alpha carbons.b. Draw a box around the R-groups.c. Circle the atoms capable of hydrogen bonding.d. Highlight the peptide bond.Mavoy bludy2. What specific atoms in your tripeptide (above) can participate in hydrogen bonding?

Amino acids are the monomers of peptides and they have two functional groups like amino group and…

Answered: 1. Draw the tripeptide: Val-Leu-Met at…

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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1. a. Draw the following pentapeptide: lysine-leucine-aspartate-threonine-phenylalanine b. Label the amino and carboxyl terminus of your peptide c. Label each amino acid residue with one and three letter abbreviations d. Label the alpha carbons e. Label the bonds around which phi and psi rotational angles occur f. Which amino acid in this chain is most likely to be phosphorylated? Which amino acid is most likely to be acetylated?
4. a. Give the full names of the amino acids in this peptide. НзN — CH—С-N—CH— С-N—CH—С—О ČH3 H ČH,OH H. CH2 -ОН b. Calculate the isoelectric point (pl) of a peptide with sequence SNARE. Show your work in a table, giving the pKa values of the ionizable groups, pH, and charges. Step marks are counted. Don't need to write “protonated" or “deprotonated".
2. Consider the peptide Trp-Arg-Glu-Cys-Gly-Tyr. For the drawings requested below, please show in zig-zag style, from amino to carboxy terminus, with correct stereochemistry a. Draw the predominant form at pH = 2 b. Draw the predominant form at pH = 5 c. Draw the predominant form at pH = 7 d. Draw the predominant form at pH = 12
6. b. Draw a box around the disulfide bridge in oxytocin, if present, or write "none". 7. Mark each peptide bond in oxytocin by making the corresponding line in the structure thicker or marking it with a different color. The first one is shown for you as an example (in dark orange). 8. Number the central carbon of each amino acid in oxytocin by pointing a small arrow to it or by circling the corresponding vertex in the image. Numbers 1 and 2 indicate the central carbons of the first and second amino acids of oxytocin, and are shown for you as an example. 9. Fill out the following table, listing amino acids that make up oxytocin in order, from the N terminus to the C terminus, characterizing each amino acid by the properties of its R group (side chains), and briefly indicating the reasoning for the characterization. You may consult amino acid groupings by category in the slides (or the textbook, p.49), but you must explain the reasoning for each in your own words. CO 1 AA# Abbre- Full…
1. What will happen if there is a change in the configuration of a protein molecule? Provide an example. 2. Give the IUPAC name for Ala-Gly-Leu
1.a.If this molecule was the side chain of an amino acid, in a protein, what tertiary structure stabilizers could be present? b.Make a key and use color to highlight what part of you structure can be stabilized in each manner?
7. A peptide has the sequence Cys-His-Glu-Met-lle-Ser-Thr a. Write out the single letter sequence of this peptide. b. What is the overall charge of the peptide? Is it acidic? Basic? c. Draw the chemical structure of the peptide at pH 7.0 and show any charged groups d. What is the classification of each amino acid in this peptide regarding polarity and charge? 8. The following proteins represent a wide range of molecular weights and isoelectricpoints. Mr is the molecular weight of a single protein chain. • Protein 1: Mr 68,544; pl 6.11 (monomer) • Protein 2: Mr 29,041; pl 5.32 (dimer) Protein 3: Mr 15,805; pl 5.7 (dimer) • Protein 4: Mr 12,165; pl 4.74 a. Which protein is the most acidic? Explain your answer. b. Which protein will migrate the slowest in an SDS-PAGE? Explain your answer. c. In what order will these proteins elute from a cation exchanger at phH 8? Explain your answer. d. In what order will these proteins salt out from a pH 7 solution by the dropwise addition of saturated…
4. Let’s build a polypeptide chain a. Using your arsenal of 4 amino acids, write out the primary structure of an 8 amino acid long polypeptide that you might be called amphipathic and thus allow it to form a micelle in aqueous solution, identify amino acid 1 through 8 as well as the location of the amino and carboxy termini of the polypeptide. b. Explain why this polypeptide would be considered amphipathic and draw what the micelle might look like in water. c. Taking amino acids 3, 4, and 5, draw the molecular structure of this particular stretch of polypeptide chain. Along the backbone linkage of the polypeptide identify the peptide bonds with a PB, the bonds with free rotation FR, and bonds with limited rotation LR.
A peptide has the sequence Gly-Ser-Lys-Ala-Gly-Gly-Arg-Ser-Arg. How many fragments would result from cleaving the sequence with trypsin? number of fragments: 3 Draw the smallest fragment at pH 7. + H₂N H O OH ZH N O _.. NH ₂
Below is the primary structure of a protein. A R 1 I I H H || O H 1 Psi bond [Select] Phi bond [Select] N-terminus [Select] B C D H O I || C-terminus [Select] NC-C-N-C-C-N-C-C-N-C-C-N-C-C - N... I 1 H H I R R H I 11 O HO I || R R I I H a. For each part of the question, select the letter associated the with appropriate component of the structure. Peptide bond [Select] I H U MO b. Which letter represents a bond without 360-degree rotation? [Select] H |
A. Write the structure of the following peptide at pH 5.0 and calculate its net charge at this pH. Asp-His-Tyr-Arg-Lys-Leu-Thr-Gln. Based on the pKa value of the ionizable groups. B. A polypeptide consisting only of L-glutamate residues (poly-L-glutamate) may have a random coil or helical structure depending on pH. Explain this behavior by indicating at what pH values the helical structure will be favored.
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

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