A/B:3. Amino acid residues and peptide bonds(a) Draw the chemical structure of F, S and H joined by peptide bonds and alsoconnected 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 drawinga 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 eachother if Psi = 0 degrees and why is this less problematic than the situation created byPhi = 0. Words and PicturesH₂N*Pka: 9.13H₂CсC._hydrophobicity:1. phenylalanine (most)2. Serine3. Histidinelleast)دهHH.HINOHICH₂CHOpka:1. Serine (nighest)2. Histidinellowest)H-NH-H₂Cpka: 1.82|сNHне-Nnucleophili city1. Serine (most)CHPka: 6.002. Histidine3. phenylalanine (least)

It is hard and hence often found confusing to explain a 3-D concept like dihedral angles in the 2-D…

Answered: 3. Amino acid residues and peptide…

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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Amino acid structure and composition: Assuming physiological pH conditions, draw the peptide backbone of a protein composed of four amino acids. The protein is a) overall positively charged b) capable of forming disulfide bond with another protein c) has two amino acid that can participate in hydrogen bond formation d) one peptide bond in cis conformation you must show the complete name, single letter abbreviation and structure of each amino acid. Make sure to highlight the peptide bond that is in cis conformation
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) (c) 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
B) An aqueous solution (pH ~7) containing mixture of three amino acids; glycine (G), arginine (R) and glutamic acid (E), was dropped onto center of a solid matrix (e.g chromatographic paper) which is incorporated in an electrical circuit (a). After applying electrostatic potential, the aminoacids are separated as shown in b. Determine amino acids that are labeled as 1, 2 and 3. a) DC Power Supply (OFF) b) DC Power Supply (ON) Solid matrix Solid matrix Cathode Anode Cathode Anode buffer buffer buffer buffer Sample containing amino acids G, R, E
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'
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.
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".
. Consider a small protein containing 101 amino acid residues. The protein will have 200 bonds about which rotation can occur. Assume that three orientations are possible about each of these bonds. (a) Based on these assumptions, about how many random-coil conforma- tions will be possible for this protein? (b) The estimate obtained in (a) is surely too large. Give one reason why.
PEPTIDE #1: Pro-Phe-Thr-Cys PEPTIDE #2: Gly-Tyr-Ser-Asp Calculate the pI of both peptides. Which is more acidic and why? Which one is more hydrophobic? Which peptide sequence (#1 or #2) would be more likely situated on the surface of the protein?
1.Here is an oligomeric protein, which has two binding sites:1)Write the formulas of side chains of amino acids which are located in binding sites and suggest two ligands,which can be bound with this protein. 2) Name the types of bonds which will be formed between the ligands and amino acids of binding sites.3)Give the definition of quaternary structure. What do you know about the properties of proteins with the quaternary structure?
The amino acid sequence of three peptide fragments are shown below. Peptide 1: QAMGRAGDLKYLGLHSV Peptide 2: ALMALFMVMALVLVSVLFIA Peptide 3: MVEDLLKQIARYLISE (a) Circle all of the charged residues in peptide 1 (assume pH =7.0). Box all of the aromatic residues in peptide 2. Underline all of the nonpolar residues in peptide 3. (b) Determine the net charge of the predominant form of each of the peptides at pH 4.5 and pH 11.5. Assume the ionizable groups have the pKa values listen in Table 2.1 of your text. (c) Which of these peptides would be most likely to be found as an alpha helix in a soluble (cytoplasmic) protein? Which would be most likely to be found as an alpha helix in a transmembrane protein? Which would be least likely to form an alpha helix of any kind?
A researcher performed an SDS-PAGE experiment (with 2- mercaptoethanol) on a mixture containing 3 peptides: (1) NAKQLEPDEYRTSC (2) EQCNLKGATCPSASWSGTQ (3) SCKRKA Note that I've bolded positively charged residues and underlined negatively charged residues In which of the gels below are the bands properly labeled? A |(1) (3) |(3) |(2) |(1) |(2) |(2) |(1) |(1) |(3) (+) (3) |(1) (2) |(3) |(2)
Name: Protein Structure 1. Draw the structure of each peptide below at pH 7.0. Using the structure, predict which peptide is more soluble in water at pH 7.0. Explain why using chemical details. RISK PALM

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