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 3, Problem 7P
Assume that some protein molecule, in its folded native state, has one favored conformation. But when it is denatured, it becomes a “random coil,” with many possible conformations.
a. If we only consider the entropy for the protein, what must be the sign of
b. How will the contribution of
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Assume that some protein molecule, in its folded native state, has onefavored conformation. But when it is denatured, it becomes a “random coil,” with many possible conformations.(a) If we only consider the change in entropy for the protein, what mustbe the sign of ΔS for the change: native → denatured? (Note: As suggestedin the next problem, this does not include solvent effects, which also make significant contributions to ΔS.)(b) How will the contribution of ΔS for native → denatured affect thefavorability of the process? What apparent requirement does this imposeon ΔH if proteins are to be stable structures?
Suppose you have a mixture of the following proteins
protein A: pl = 3.5, mw = 35 kDa
protein B: pl = 5.5, mw = 22 kDa
protein C: pl = 7.5, mw = 77 kDa
protein D: pl = 9.0; mw = 52 kDa.
Which protein do you expect to elute last if you perform separation using cation
exchange chromatography at pH 7.0?
A
B
Oc
The dissociation constant, Kd for a complex between protein A and protein B is 4.1 μM. If the two proteins are mixed together at initial concentrations of [A]= 0.025 μM and [B] = 4.7 μM, calculate (a) the equilibrium concentrations of A, B, and AB (the dimer formed by A and B) (b) the percentage of A bound to B
Chapter 3 Solutions
Biochemistry: Concepts and Connections (2nd Edition)
Ch. 3 - Prob. 1PCh. 3 - Given the following reactions and their...Ch. 3 - The decomposition of crystalline N2O5...Ch. 3 - The oxidation of glucose to CO2 and water is a...Ch. 3 - Prob. 5PCh. 3 - In another key reaction in glycolysis,...Ch. 3 - Assume that some protein molecule, in its folded...Ch. 3 - When a hydrophobic substance like a hydrocarbon is...Ch. 3 - It is observed that as temperature is increased,...Ch. 3 - Suppose a reaction has Ho and So values...
Ch. 3 - Prob. 11PCh. 3 - Prob. 12PCh. 3 - Prob. 13PCh. 3 - Undergoing moderate activity, an average person...Ch. 3 - The major difference between a protein molecule in...Ch. 3 - Prob. 16PCh. 3 - Prob. 17PCh. 3 - Consider the degradation of glucose to pyruvate by...Ch. 3 - a. Consider the malate dehydrogenase reaction,...Ch. 3 - Bovine ribonuclease folds with Ho = -280 kJmol-1...
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- The major difference between a protein molecule in its native state and in its denatured state lies in the number of conformations avail- able. To a first approximation, the native, folded state can be thought to have one conformation. The unfolded state can be estimated to have three possible orientations about each bond between residues. (a) For a protein of 100 residues, estimate the entropy change per mole upon denaturation. (b) What must be the enthalpy change accompanying denaturation to allow the protein to be half-denatured at 50 °C? (c) Will the fraction denatured increase or decrease with increasing temperature?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_forwardConsider olive oil, an oil with a high percentage of fat derived from oleic acid (otherwise known as cis[18:1] fatty acid). a, Explain why such a structure may allow olive oil to be one of the "healthier" oils? b, why such a structure may allow olive oil to be a liquid at room temperature, while butter and lard are solid at room temperature? c, why such a structure may cause olive oil to be prone to oxidative damage upon exposure to air and heat?arrow_forward
- If your initial absorbance from undiluted crude dialysate is 4.50, determine the fold dilution needed to yield an absorbance of approximately 0.700. If you want to prepare 1.0 ml of diluted crude, what volume (mL) of crude dialysate must you add? Your Answer: Answer units It is possible to estimate the molar extinction coefficient of a protein from knowledge of its amino acid composition, as shown from your experiences with EXPASY. From the molar extinction coefficient of tyrosine, tryptophan and cystine (cysteine does not absorb appreciably at wavelengths >260 nm, while cystine does) at a given wavelength, the extinction coefficient of the native protein in water can be computed using the following equation: e(Protein) = #(Tyr)*E(Tyr) + #(Trp)*E(Trp) + #(Cystine)*E(Cystine) Where (if A280 measured in water): E (Tyr) = 1490, ɛ (Trp) = 5500, e (Cystine) = 125 Estimate the molar extinction coefficient of lysozyme using the above equation and the amino acid composition data you found…arrow_forwardTwo common methods of denaturing proteins in the lab are to increase the temperature and/or add chemical denaturants like the detergent SDS (shown below). Describe how each of these processes (heating and addition of SDS) disrupts the forces and interactions that stabilize the native state, leading to unfolding. The answer should include a discussion of the Gibbs free energy of folding, enthalpy, and entropy.arrow_forwardSupported lipid bilayers (SLBs) are widely used in biophysical research to investigate the effect of drugs on lipid membranes and may be prepared by different methods. a. State two methods for the formation of SLBs. b. Describe, with the aid of diagrams, one of the previously stated methods for preparing SLBs. Provide any experimental conditions that may affect or promote the formation of the SLB.arrow_forward
- Consider the dissociation reaction for a protein-ligand complex: P•L P + L A. Sketch a binding curve (fractional saturation θ vs. ligand concentration [L]) for this protein-ligand complex (ligand A). Show where on that curve you could obtain the dissociation equilibrium constant Kd for the reaction. B. Now sketch on the same axes a θ vs. [L] plot for a different ligand (B) that binds more weakly than the first ligand. C. Does the weaker binding ligand have a higher, or lower, Kd than the tighter binding ligand? D. Sketch a binding curve for a cooperatively bound ligand with K0.5 higher than that of Kd for A or B. (Note: for cooperative binding, each protein molecule would have to have more than 1 binding site for the ligand; K0.5 is the experimentally determined ligand concentration that gives θ = 0.5.)arrow_forwardImagine there is a beaker with a solution containing 1,000 hemoglobin homotetramers and 1,000 protons (H*). Which of the statements concerning the concerted and sequential models is NOT true if you assume only 1 proton is capable of binding 1 hemoglobin monomer? Select one: a. If an additional 1,000 protons were added, according to the concerted model, all of the homotetramers will adopt the R state. b. According to the concerted model, the addition of protons will cause an increase in the number of tetramers in the T state. c. According to the sequential model, there will be some monomers of homotetramers in the R state and some in the T state. d. If an additional 2,000 protons were added, according to the sequential model, there will be a greater proportion of hemoglobin in the T state. е. If an additional 2,000 protons were added, according to the concerted model, more hemoglobin will adopt the T state.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_forward
- The major difference between a protein molecule in its native state and inits denatured state lies in the number of conformations available. To a firstapproximation, the native, folded state can be thought to have one conformation. The unfolded state can be estimated to have three possible orientations about each bond between residues.(a) For a protein of 100 residues, estimate the entropy change per moleupon denaturation.(b) What must be the enthalpy change accompanying denaturation to allow the protein to be half-denatured at 50 °C?(c) Will the fraction denatured increase or decrease with increasingtemperature?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). (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.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).(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.arrow_forward
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