Biochemistry
9th Edition
ISBN: 9781319114671
Author: Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.
Publisher: W. H. Freeman
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Chapter 2, Problem 11P
Interpretation Introduction
Interpretation:
The graph of concentration versus pH for histidine should be determined and the structures of each individual species should be drawn.
Concept introduction:
The ionization of an amino acid depends on the pH. In acidic pH both amino group and carboxylate group are protonated. When pH increases, the
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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.
a. Suppose that you have the peptide Ala-Gly-Tyr-His-Leu and you treat it with FDNB and then 6M HCl. Draw the structures of all the products that you will have in solution (assume all reactions to go to completion).
. Give two reasons to explain why a proline residue in the middle of an ahelix is predicted to be destabilizing to the helical structure
Chapter 2 Solutions
Biochemistry
Ch. 2 - Prob. 1PCh. 2 - Prob. 2PCh. 2 - Prob. 3PCh. 2 - Prob. 4PCh. 2 - Prob. 5PCh. 2 - Prob. 6PCh. 2 - Prob. 7PCh. 2 - Prob. 8PCh. 2 - Prob. 9PCh. 2 - Prob. 10P
Ch. 2 - Prob. 11PCh. 2 - Prob. 12PCh. 2 - Prob. 13PCh. 2 - Prob. 14PCh. 2 - Prob. 15PCh. 2 - Prob. 16PCh. 2 - Prob. 17PCh. 2 - Prob. 18PCh. 2 - Prob. 19PCh. 2 - Prob. 20PCh. 2 - Prob. 21PCh. 2 - Prob. 22PCh. 2 - Prob. 23PCh. 2 - Prob. 24PCh. 2 - Prob. 25PCh. 2 - Prob. 26PCh. 2 - Prob. 27PCh. 2 - Prob. 28PCh. 2 - Prob. 29PCh. 2 - Prob. 30PCh. 2 - Prob. 31PCh. 2 - Prob. 32PCh. 2 - Prob. 33PCh. 2 - Prob. 34PCh. 2 - Prob. 35PCh. 2 - Prob. 36PCh. 2 - Prob. 37P
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- Peptides. 1. Draw the peptide Ala-Glu-Gly-Lys, as it would occur at physiological pH = 7.4. The R groups of Ala and Gly are not acidic or basic, therefore do not have a pka and the charge on these R groups is therefore independent of pH. Glu is acidic and Lys is basic, therefore the charge on these amino acids is pH dependent. The pKas are shown below. pKa N-term = 9.0 C-term = 3.5 Glu4.1 Lys = 10.5 2. Draw a circle around the peptide bonds. 3. Label the C-terminus and the N-terminus. 4. What is the overall charge on the peptide at pH 7.4?arrow_forwardAsp-Gly-Lys-Glu-Ile-Phe Draw its full chemical structure as it would exist at pH = 7.0. Draw an arrow pointing to each peptide bond. Identify the net charge of the peptide and briefly explain how you arrived at this answer.arrow_forwardR V. Phospholipids are the main structural lipids that comprise cellular and organellar membranes. One abundant phospholipid in bacterial cell membranes is phosphatidylethanolamine (PE), which has a generic structure shown on the right. Note that R1 R and R2 are representative alkyl chains of attached fatty acids, each having about 16 – 20 carbon atoms. a) The overall net charge in one PE molecule is: -2 -1 0 +1 +2 CH₂ Phosphatidylethanolamine (PE) -CH H₂C. b) The glycerophosphate backbone in PE is a: D-enantiomer c) The fatty acids are attached to PE via which type of bond? amine L-enantiomer racemic NH3 amide ester ether d) Draw the commonly used cartoon representation of one phospholipid molecule. Label the hydrophilic and hydrophobic parts.arrow_forward
- Suppose you have a solution of a protein, which contains a specific Tyr residue that has an actual (measured) pKa of 8.8. The protein binds a ligand by several noncovalent interactions, one of which is a hydrogen bond in which the Tyr phenolic hydroxyl group must serve as a hydrogen bond donor. Calculate the percentage of the protein molecules in which that tyrosyl residue's phenolic hydroxyl group could serve as a hydrogen bond donor at pH 8.5arrow_forwardConsider the phenolic hydroxyl group of a particular Tyr residue in a protein. Suppose the hydroxyl group in the unfolded protein in aqueous solution, where the group is exposed to H2O, has a pKa of 10.0. If that group is found in a hydrophobic environment in the interior of the protein when the protein is folded into its native tertiary structure, would you expect the pKa of the phenolic hydroxyl to be higher or lower in the folded protein interior than in H2O? Explain your reasoning.arrow_forwardDescription Please draw the structure of the 19 L-a-amino acids and proline in any form, as you prefer. You may want to use a letter-size sheet or larger, it's up to you. Guiding principle: You want to understand the differences among amino acids. Although you may want to only draw the R-group it's preferable to draw it along with the rest of the molecule (i.e., the Ca, the amino group and the carboxyl group). Here are some examples (your drawings should not limited to the following styles): H₂C NH₂ OH shutterstock.com-222977980 Alanine H H Proline OH %%% lysine a alamy stock photo Tryptophan HN NH₂ shutterstock.com-1819000134 QH COOH H₂N-C- H CH ₂ Phenylalanine H₂N NH dreamstime.com arginine NH₂ OHarrow_forward
- A schematic diagram of the helical structure of cytochrome b562 is reproduced below. Thisprotein belongs to the family of -proteins that have a four-helix bundle. Number the helices 1 – 4according to their N C direction. Indicate relative orientations of the macrodipoles of helices 1 – 4adjacent to the diagram of cytochrome b562. Remember that according to the definition of a dipolethat the arrow points towards the positive end.arrow_forwardDraw any pentapeptide. All C-O, C-N, and C-S bonds must be written out, as well as all N-H, S-H, and O-H atoms/bonds. Your peptide must include at least one amino acid from each of the major classes of amino acids (i.e. charged, polar, etc.). Circle each peptide bond in this peptide.arrow_forwarda All amino acids have at least two ionizable groups: an a-amino group (average pK₁ of 8.0) and an α-carboxylic acid group (average pK₂ of 3.1). Histidine also has an ionizable side chain (R group) with a pKa of about 6.0. One of the possible ionization states of histidine is shown in a the image. Select the pH values at which the charged form of the R group would predominate. 6.0 At what pH would the structure shown be the predominant ionization state? Consider the ionization state of all three of the functional groups. 2.2 + The protonated form of the R group of histidine is shown in the structure. The ratio of the charged (protonated) form to the deprotonated form depends on the pK₁ of the R group and the pH of the solution. 4.9 H₂N-CH-C-OH | CH₂ 11.5 + HN -NHarrow_forward
- 4. A. Draw the structure of the following peptide sequence at pH 2.0: ASP-ALA-THR-LYS-GLY B. What is the net charge of this pentapeptide at pH 2.0?arrow_forwarda. 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_forwardUsing Haworth projections, how can I draw a hetero trisaccharide containing two different types of glycosidic bonds? Also provide the names of each monosaccharide in the chain.arrow_forward
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