Biochemistry: Concepts and Connections (2nd Edition)
2nd Edition
ISBN: 9780134641621
Author: Dean R. Appling, Spencer J. Anthony-Cahill, Christopher K. Mathews
Publisher: PEARSON
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Chapter 2, Problem 22P
Consider a protein in which a negatively charged glutamic acid side chain (pks = 4.2) makes a salt bridge (ion—ion interaction) with a positively charged histidine side chain (pKa = 6.5).
a. Do you predict that this salt bridge will become stronger, become weaker, or be unaffected as pH increases from pH = 7.0 to pH = 7.5?
b. Justify your answer with calculations of partial charges on these amino acid side chains. (Hint Consider lessons from Coulomb's law, and the Henderson-Hasselbalch equation)
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Consider a protein in which a negatively charged glutamic acid side chain(pKa = 4.2) makes a salt bridge (ion–ion interaction) with a positively charged histidine side chain (pKa = 6.5).(a) Do you predict that this salt bridge will become stronger, become weaker, or be unaffected as pH increases from pH = 7.0 to pH = 7.5?(b) Justify your answer with calculations of partial charges on these aminoacid side chains.
Consider a protein in which a negatively charged glutamic acid side chain (pKa = 4.2) makes a salt bridge (ion–ion interaction) with a positively charged histidine side chain (pKa = 6.5). (a) Do you predict that this salt bridge will become stronger, become weaker, or be unaffected as pH increases from pH = 7.0 to pH = 7.5? (b) Justify your answer with calculations of partial charges on these amino acid side chains.
For the following pentapeptides: Ser-Glu-Gly-His-Ala and Gly-His-Ala-Glu-Ser
A. Compute their isoelectric pH (pI). Show full solution. Use standard pKa values.
B. Do these peptides with the same amino acid composition have different net charges at pH 7.0? Explain briefly.
C. Would you expect the titration curves of the two peptides to differ? Why or Why not?
Chapter 2 Solutions
Biochemistry: Concepts and Connections (2nd Edition)
Ch. 2 - Suppose a chloride ion and a sodium ion are...Ch. 2 - Draw two different possible hydrogen-bonding...Ch. 2 - Prob. 3PCh. 2 - 4. What is the pH of each of the following...Ch. 2 - Prob. 5PCh. 2 - The weak acid HA is 2% ionized (dissociated) in a...Ch. 2 - 7. Calculate the pH values and draw the titration...Ch. 2 - What is the pH of the following buffer mixtures?...Ch. 2 - a. Suppose you wanted to make a buffer of exactly...Ch. 2 - Prob. 10P
Ch. 2 - You need to make a buffer whose pH is 7.0, and you...Ch. 2 - Describe the preparation of 2.00 L of 100 glycine...Ch. 2 - Carbon dioxide is dissolved in blood (pH 7.4) to...Ch. 2 - What is the molecular basis for the observation...Ch. 2 - The anno acid arginine ionizes according to the...Ch. 2 - It is possible to make a buffer that functions...Ch. 2 - A student is carrying out a biological preparation...Ch. 2 - Histidine is an amino acid with three titratable...Ch. 2 - Prob. 19PCh. 2 - A biochemical reaction takes place in a 1.00 ml...Ch. 2 - Is RNA-binding enzyme RNase A more likely to have...Ch. 2 - Consider a protein in which a negatively charged...Ch. 2 - Prob. 23PCh. 2 - Prob. 24P
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- Consider a protein in which a negatively charged glutamic acid side chain (pKa = 4.2) makes a salt bridge (ion-ion interaction) with a positively charged histidine side chain (pKa = 6.5). Part A Do you predict that this salt bridge will become stronger, become weaker, or be unaffected as pH increases from pH = 7.2 to pH = 7.8? The salt bridge will become stronger. The salt bridge will become weaker. The salt bridge will be unaffected. Submit Part B Previous Answers Correct At pH = 7.2 the glutamic acid (Glu) side chain will carry a charge of ~ -1 (at 3 pH units above the pKa for Glu, the side chain will be almost fully ionized); whereas the histidine (His) side chain will carry a charge of < +0.5 (at pH = pK₂ the charge on His would be +0.5; since pH = 7.2 is above its pKa, it will carry less (+) charge as it becomes more deprotonated). As the pH increase to 7.8, the charge on Glu will remain ~ -1 and the charge on His will decrease; thus, this salt bridge is predicted to become weaker…arrow_forwardConsider a protein in which a negatively charged glutamic acid side chain (pKa=4.2) makes a salt bridge (ion-ion interaction) with a positively charged histidine side chain (pKa=6.5). Part C: Justify your answer with calculations of partial charges on these amino acid side chains at pH=7.9.(Hint: Consider lessons from Coulomb's law, and the Henderson-Hasselbalch equation.)arrow_forwardConsider a peptide with the sequence Ala-Glu-Arg-Leu. Assume the ionizable groups have the pKa values listed in Table 2.1 of your text. (a) Draw the predominant ionic form of the peptide at pH 7.4. (b) Determine the net charge of the predominant form of the peptide at pH 7.4. (c) Calculate the pI of the peptide.arrow_forward
- A protein has molecular mass of 200 kDa when measured by gel filtration. When subjected to SDS PAGE with and without 2-mercaptoethanol (2-ME) the gel shown below was obtained. What is the likely subunit composition of this protein and why? a. The protein has 4 subunits, with molecular masses 100, 50, 25, and 25 kDa. 25 kDa subunits are linked to each other via noncovalent interactions. b. The protein has 4 subunits, with molecular masses 100, 50, 25, and 25 kDa. 50 kDa subunit is linked to the one 25 kDa subunit via noncovalent interactions. c. The protein has 3 subunits, with molecular masses 100, 75 and 25 kDa that are linked by noncovalent interactions. d. The protein has 4 subunits, with molecular masses 100, 75, 50 and 25 kDa. The subunits are linked by disulfide bonds. e. The protein has 4 subunits, with molecular masses 100, 50, 25, and 25 kDa. 50 kDa subunit is linked to the one 25 kDa subunit by disulfide bonds.arrow_forwardConsider a protein in which a negatively charged glutamic acid side chain (pKa=4.2)(pKa=4.2) makes a salt bridge (ion-ion interaction) with a positively charged histidine side chain (pKa=6.5)(pKa=6.5).arrow_forwardUsing the data in Table calculate the average amino acid residue weight in a protein of typical composition. This is a useful number to know for approximate calculationsarrow_forward
- You have a peptide that has the following amino acid sequence: GPMG Draw the structure of the polypeptide's most protonated form, and its charge. Then draw the structures of the increasingly deprotonated forms, along with their charges. Use the information from these structures to calculate the pl (isoelectric point) of the peptide using the pKa values provided in the table below. Write the pl as x.yz, for example, 7.62 or 3.09. Group Terminal a carboxyl group Aspartic acid Glutamic acid Histidine Terminal a-amino group Cysteine Lysine Tyrosine Arginine Acid EM 2-0" + H -N H H N-H H N-H T Base 1 1. تر H -5 H H O™ N-H Typical pK, 3.1 4.1 6.0 8.0 8.3 10.8 10.9 12.5arrow_forwardGiven the following Peptide: Q6 *H;N-Phe-Asp-Ala-Arg-Gy-His-Arg-Asp-Glu-His-Tyr-CO 6a. What is the peptide's net charge at pH 2.0, pH 6.0, pH 7.4, and pH 10.2? (show work) 6b. What is the approximate isoelectric point of this peptide?arrow_forwardA peptide has the sequence: Glu–His–Trp–Ser–Gly–Leu–Arg–Pro–Gly1. What would be the net charge of the molecule at pH a) 3, b) 8, and c) 11? (Use pKa values. Do not calculate the value per se, but instead estimate considering only fully protonated, or deprotonated states. Then estimate the pI for this peptide. Show full, clear and complete procedurearrow_forward
- Two peptide sequences are shown below.Peptide A: N-term – GDL – C-termPeptide B: N-term – GTL – C-terma. Draw each peptide at physiological pH. Circle each ionizable functional group in your drawing.b. Briefly explain why changing aspartate to threonine changes the number of ionizable functionalgroups in the peptide chain.c. Briefly explain why the functional group found in aspartate’s side chain is ionizable but the functionalgroup found in threonine’s side chain is not.arrow_forwardProtein A is made up of a single polypeptide chain; The molecular mass of A is 20,000 Da; the A molecule has 2 tryptophan residues, 5 tyrosine residues, and no disulfide bonds. Calculate what absorbance (at 280 nm) a solution of protein A will have at a concentration of 1.0 mg / mL, in a 1 cm cell. Write the calculations you have done.arrow_forwardA. 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.arrow_forward
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