The most important contribution to the stability of a protein's conformation appears to bethe:○ A) entropy increase from the decrease in ordered water molecules forming a solvent shell around itO B) large entropy increase from ionic interactions between the ionized amino acids in a proteinC) sum of the free energies of many weak interactions among the hundreds of amino acids in a protein○ D) sum of free energies of formation of many weak interactions between polar amino acids andsurrounding waterE) stabilizing effect of hydrogen bonding between the carbonyl group of one peptide bond and theamino group of another

The most important contribution to the stability of a protein's conformation appears to be the:…

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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

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The most important contribution to the stability of a globular protein's conformation appears to be the: a.) entropy increase from the decrease in ordered water molecules forming a solvent shell around it. b.) maximum entropy increase from ionic interactions between the ionized amino acids in a protein. c.) sum of free engeries of formation of may weak interactions between its polar amino acids and surrounding water.
Protein denaturation usually refers to the disruption of which of the following types of molecular interactions? Select all that apply. A.)Van der Waals attraction B.)Covalent bonds C.)Hydrogen bonds D.)Hydrophobic interactions
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?
b) The likelihood of both triglycerides and phospholipids to behave as liquids at a given temperature is affected by their degree of saturation. Explain what saturation is and provide a biochemical explanation for why it affects the likelihood of a lipid to behave as a liquid at a given temperature. 5) a) Proteins have multiple "levels" of structural complexity. Match the type of chemical bond on the left with the level of protein structure that they are specifically involved in maintaining on the right. (Note that more than one letter may apply to each structural level and that each letter may be used more than once or not at all). a. disulphide bonds Tertiary structure b. hydrogen bonds Primary structure c. ionic bonds Quaternary structure d. peptide bonds Secondary structure
How do the following noncovalent interactions help to stabilize the tertiary and quaternary structure of a protein? Give an example of a pair of amino acids that could giverise to each interaction.(a) Hydrophobic interactions(b) Salt bridges (ionic interactions)
Based on this table: 1) What is the difference between subunit mass and native mass? 2) How do you tell what the likely quarternary structure of the protein is? (heterotrimer, homotrimer, etc.)
Which reagent(s) would you use for the following processes related to protein chemistry? Write the respective equations. a) Identification of the terminal amino residue. b) Determination of the amino acid sequence of the peptide Gly-Asp-Ala-Cys c) Reversible denaturation of a protein containing disulfide bonds d) Hydrolysis of peptide bonds of aromatic residues of a protein e) Fragmentation of a protein by breaking peptide bonds on the carbonyl side of methionines.
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?
Φ and ψ in the Ramachandran plot (below) are: a) Rotational angles around the bond between the α-carbon and N-H (Φ) and C=O (ψ). b) Amino acid solubility in octanol (Φ) and water (ψ). c) Hydrogen bond angles in α-helices (Φ) and β-sheets (ψ). d) Amino acid solubility in water (Φ) and octanol (ψ).
What is the charge of the primary structure of proteins at pH = 2.0, 4.0,6.0 and 11.0 of the following proteins. Draw their structures and predict their net 1. charge. A) Lys- Gly- Ala- Gly B) Lys- Gly-Ala-Glu C) His- Gly- Ala- Glu D) Glu- Gly- Ala -Glu E) Gln-Gly-Ala-Lys 2. Calculate the pI of the following primary structure of protein 3. the migration toward the cathode, the negative pole; A for the migration toward the anode, the positive pole; and o if the peptide remains stationary.
1)Explain 3 benefits of proteins forming higher oligomeric states. 2) Why are peptide bonds planar?
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 change in entropy for the protein, what must be the sign of ∆S for the change: native → denatured? (Note: As suggested in the next problem, this does not include solvent effects, which also make significant contributions to ∆S.) (b) How will the contribution of ∆S for native → denatured affect the favorability of the process? What apparent requirement does this impose on ∆H if proteins are to be stable structures?

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