3A. For the following tripeptide, provide its full name, abbreviated name, describe what type of interactions would be present in the tertiary structure of a protein that contains this sequence. In other words, evaluate what types of interactions can occur between the amino acids provided in this peptide and the functional groups in different amino acid side chains. How would this peptide interact with water? Explain why Full Name: Abbreviated Name: Interactions: Interactions with water: H. H3N-CHC-N-CHC-N-CHC-O CH2 CH2 CH2 CH2 O NH3 CH2 CH2 OH NH

3A. For the following tripeptide, provide its full name, abbreviated name, describe what type of interactions would be present in the tertiary structure of a protein that contains this sequence. In other words, evaluate what types of interactions can occur between the amino acids provided in this peptide and the functional groups in different amino acid side chains. How would this peptide interact with water? Explain why Full Name: Abbreviated Name: Interactions: Interactions with water: H. H3N-CHC-N-CHC-N-CHC-O CH2 CH2 CH2 CH2 O NH3 CH2 CH2 OH NH

Biology 2e

2nd Edition

ISBN:9781947172517

Author:Matthew Douglas, Jung Choi, Mary Ann Clark

Publisher:Matthew Douglas, Jung Choi, Mary Ann Clark

Chapter3: Biological Macromolecules

Section: Chapter Questions

Problem 23CTQ: Amino acids have the generic structure seen below, where R represents different carbon-based side...

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1. Which peptide would be more soluble at pH 7.0, (Val)₂₀ or (Asp)₂₀ ? at pH 3.0, (Gly-Glu-Val)
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?
2. A group of peptides that influence nerve transmission in certain parts of the brain have been isolated from normal brain tissue. These peptides are known as opioids. Using the information below, determine the amino acid sequence of this particular opioid: ● Complete hydrolysis by HCl at 100° C followed by amino acid hydrolysis analysis indicated the presence of Gly, Leu, Phe, and Tyr, in a 2:1:1:1 ratio. ● Treatment of the peptide with FNDB followed by complete hydrolysis indicated the presence of 2,2-dinitrophenyl derivative of tyrosine. No free tyrosine could be found. ● Complete digestion of the peptide with chymotrypsin yielded free tyrosine and leucine, plus a tripeptide containing Phe and Gly in a 1:2 ratio. Instructions Make use of the table below to determine the sequence of the mystery protein:
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?
1. In a protein, why does when Ala is replaced with Ile, it loses its activity but when Lys is replaced by Arg and Leu to Ile, it only has little effect on protein structure and function? Explain. 2. Why do proteins cannot be denatured reversibly when they are chemically altered to change the chemical composition of certain side chains? Explain.
* Draw the tripeptide FTQ, making sure to care for stereochemistry.* Identify the N-terminus and the C-terminus of the peptide.* Identify what type of stabilizing interactions the amino acid side chains could employ in the tertiary andquaternary structure of a protein.
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. Write the structure of each of the following peptides at pH 7: a. Alanylphenylalanine b. Threonylcysteine c. Phenylalanyltryrosylleucine d. Glycylvalylserine 5. Tripeptides are composed of three amino acids linked by peptide bonds. Given a set of amino acids, you can make several different tripeptides. a. Use the three-letter shorthand notations to name all the tripeptides that can be made from serine, tyrosine, and glycine. Each amino acid will be used once in each tripeptide. b. Draw the complete structure of the tripeptides that have glycine as the N-terminal amino acid.
1. In the separation of lysine from histidine using a sulfonated polystyrene column will it be easier to separate at pH 4 or pH 8 ? explain! 2. A peptide of the order Glx-Ala-Gly-Arg bound to a sulfonated polystyrene column at neutral pH. Is Glx Glu or Gln ? Explain !
Which intermolecular forces are important in acetic acid, CH3 –(C=0)-oh? A particular amino acid contains a- CHNH3+ group. Is this amino acid more likely to be found on the inside or the outside of the folded protein? Briefly explain. The addition of ethanol, CH3CHOH, t an aqueous solution lowers the surface tension of the solution. Predict whether adding ethanol to an aqueous protein solution will tend to stabilize or unfold the protein. Briefly explain.
a) Where is the N-terminus of this peptide? Left Middle Right b) What type of secondary structure is the majority of this structure? loops alpha helix Beta sheet unstructured c) The X's indicate the alpha carbons of residues 10, 13, and 17 (labeled in the sequence above). Where would you expect this part of the structure to be found in the tertiary structure of the protein? Briefly explain your reasoning. d) The dashed line in black is indicating an interaction that is present within this structure. Draw this interaction, including all the atoms necessary for this interaction to occur. Label any partial charges present in your drawing. please upload the drawing.
1. Sickle cell anemia results from a substitution of a valine for a glutamic acid. What do you expect the effect might be if the mutation were to have placed a leucine at that site? An aspartic acid? 2. Of the following amino acids, glycine, isoleucine, and lysine, which would you expect to be the most soluble in an acidic aqueous solution? Which the least? 3. How many structural isomers could be formed from a molecule with the formula C5H12? C4H8?