11. Below is a folding energy funnel describing folding energy landscape of a protein. The width of thefunnel indicates the entropy of the protein, and the height corresponds to the free energy.A) If A is the native fold structure, which state is a moltenglobule? How does this state differ from A in term ofstructures.B) Does this protein have multiple folding pathways orjust one?C) which state has the lowest free energy?D) According to the width of the funnel, the native stateBof the protein has the lowest entropy. If the protein foldAspontaneously to this state, does it violate the 2nd law of thermodynamics? Why or why not? (Hint: inthe folding funnel, only the entropy of the protein alone is considered).E) Does the native state also have the lowest enthalpy. What makes the enthalpy decrease as theprotein folds?12. List four methods by which a protein can be denatured and briefly describe how these methodsact to disrupt protein structure.

B) Folding Pathways:The protein has multiple folding pathways within the funnel. Imagine a funnel…

Answered: 11. Below is a folding energy funnel…

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

See similar textbooks

Similar questions

1. What are the effects of a) amino acid composition and sequence and b) intramolecular and intermolecular forces of attraction to protein folding? 2. What molecular property of amino acids can be used to justity the concept that the "molecular part of the protein can exhibit the same property as the molecular 'whole' (protein molecule?). Provide a comprehensive discussion using one molecular property. 3. Discuss two metabolic disorders which are caused by protein misfolding. Explain the metabolic consequence of the disorder. 4. If a non-science person asks you what protein folding is and how the concept is related to metabolic disorders, how are you going to explain the concept? (please summarize the concepts used, thank you!)
9. A) Please write down the names of the following protein folds. A B C B) Which one(s) is made of more than one polypeptide? D E 000 C) Give an example of a protein containing the motif in C and explain how the structure of this motif facilitates function. 10. What is Levinthal's paradox? Describe the paradox and explain the conclusion to which it led.
The major difference between a protein molecule in its native state and in its denatured state lies in the number of conformations available. To a first ap- proximation, the native, folded state can be thought to have one conforma- tion. The unfolded state can be estimated to have three possible orientations about cach 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?
. 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) What must be the sign of AS for the change: native → denatured? (b) How will the contribution of AS for native → denatured affect the favorability of the process? What apparent requirement does this impose on AH if proteins are to be stable structures?
4) For various amino acid pairs (for example: F to A, E to R, D to N, V to L, S to W), ask yourself: a) Based on what you know about the chemical properties of the side chains, what effect would you expect on the stability of the protein if you mutated one residue of the pair into the other in the interior of the protein? What forces might have an impact on this change (ie: what types of interactions would you expect that amino acid to be involved in?) How would your answer change if the amino acid were located on the surface of the protein? b) c)
In the article the authors reference the canonical forces in protein folding. Describe how these forces make folding an energetically favorable process. Why do the authors suggest that other intermolecular interactions must be important to fully understand folding processes?
The process of a protein folding from an inactive unfolded structure to theactive folded structure can be represented by the following equation: unfolded protein ⇌ folded proteinThe values of ΔH° and ΔS° for the folding of the protein lysozyme are: ΔH ° = -280 kJ/ mol ΔS ° = -790 J/mol • K(a) Calculate the value of ΔG° for the folding of lysozyme at 25 °C.(b) At what temperature would you expect the unfolding of lysozyme tobecome favorable? (c) At what temperature would the ratio of unfolded protein to foldedprotein be 1:5?
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?
Currently, aspartic acid is forming an ionic interaction with arginine in a protein. Part a) If arginine is replaced with glutamic acid, would the ionic interaction have its stability increased, decreased, or have no effect on the ionic interaction? Part b) If arginine is replaced with Lysine, would the ionic interaction have its stability increased, decreased, or have no effect on the ionic interaction? Part c) If arginine is replaced with isoleucine, would the ionic interaction have its stability increased, decreased, or have no effect on the ionic interaction?
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'
Which of the following (could be more than one) would not be a rational explanation for why the three-dimensional structure of a protein is driven and stabilized largely by noncovalent rather than covalent bonds?a) Proteins may be degraded for energy, and if their three-dimensional structures were heldtogether by mostly covalent bonding, this might be too difficult to accomplishb) Proteins will need to be unfolded to cross biological membrane, and if their three-dimensionalstructures were held together by mostly covalent bonding, this might be too difficult toaccomplish.c) Protein function (transport, enzyme catalysis, etc...) may require flexibility in the three-dimensional structure to allow for conformational change, and if protein three-dimensionalstructure were held together by mostly covalent bonding, this might be too difficult toaccomplish.d) All of the answer choices are rational explanations for why the three-dimensional structure of protein is driven and stabilized largely…
Which statement is true about protein folding? ○ The equilibrium between folded and unfolded states is best determined by measuring the time course of unfolding ○ Refolding of a protein typically exhibits a linear dependence on the concentration of denaturant ○ The sigmoidal shape of the unfolding transition reflects the complex architecture of proteins ○ Proteins with stable folding intermediates usually exhibit smooth free-energy funnels ○ The rate of unfolding increases as the temperature increases towards the Tm value

SEE MORE QUESTIONS

Recommended textbooks for you

Biochemistry

ISBN:

9781319114671

Author:

Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Publisher:

W. H. Freeman

Lehninger Principles of Biochemistry

Biochemistry

ISBN:

9781464126116

Author:

David L. Nelson, Michael M. Cox

Publisher:

W. H. Freeman

Fundamentals of Biochemistry: Life at the Molecul…

Biochemistry

ISBN:

9781118918401

Author:

Donald Voet, Judith G. Voet, Charlotte W. Pratt

Publisher:

WILEY

Biochemistry

ISBN:

9781319114671

Author:

Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Publisher:

W. H. Freeman

Lehninger Principles of Biochemistry

Biochemistry

ISBN:

9781464126116

Author:

David L. Nelson, Michael M. Cox

Publisher:

W. H. Freeman

Fundamentals of Biochemistry: Life at the Molecul…

Biochemistry

ISBN:

9781118918401

Author:

Donald Voet, Judith G. Voet, Charlotte W. Pratt

Publisher:

WILEY

Biochemistry

ISBN:

9781305961135

Author:

Mary K. Campbell, Shawn O. Farrell, Owen M. McDougal

Publisher:

Cengage Learning

Biochemistry

ISBN:

9781305577206

Author:

Reginald H. Garrett, Charles M. Grisham

Publisher:

Cengage Learning

Fundamentals of General, Organic, and Biological …

Biochemistry

ISBN:

9780134015187

Author:

John E. McMurry, David S. Ballantine, Carl A. Hoeger, Virginia E. Peterson

Publisher:

PEARSON

SEE MORE TEXTBOOKS