64. Cooperativity in the unfolding process during protein denaturation suggests that loss of A. Conformation of a protein segment is coupled with gain by another B. Function of a single protein affects the overall protein class activities C. Structure in one area of a protein affects the stability of other areas D. Working conformations of proteins leads to increase in their stability 65. Which of the following denaturants acts by significantly changing the net charges of polar amino acid residues in proteins? A. Acids B. Alcohols C. Detergents D. Disulfides

64. Cooperativity in the unfolding process during protein denaturation suggests that loss of A. Conformation of a protein segment is coupled with gain by another B. Function of a single protein affects the overall protein class activities C. Structure in one area of a protein affects the stability of other areas D. Working conformations of proteins leads to increase in their stability 65. Which of the following denaturants acts by significantly changing the net charges of polar amino acid residues in proteins? A. Acids B. Alcohols C. Detergents D. Disulfides

Biochemistry

6th Edition

ISBN:9781305577206

Author:Reginald H. Garrett, Charles M. Grisham

Publisher:Reginald H. Garrett, Charles M. Grisham

Chapter31: Completing The Protein Life Cycle: Folding, Processing, And Degradation

Section: Chapter Questions

Problem 3P: Understanding the Relevance of Chaperones in Protein Folding Protein molecules, like all molecules,...

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Loop regions play important roles in the secondary structure of protein. Define loop region and give three (3) of the roles
-100 100 8. This is a helical wheel projection. The following amino acids of your protein were predicted to participate in an alpha helix: DRMVEHACKSI. a. Plot these amino acids in the helical wheel projection below. b. Is the alpha helix in your protein hydrophobic, amphipathic or hydrophobic? c. Would you expect this helix to be on the interior of the protein, exposed, or partially exposed?
2. A ligand binds more tightly to the folded state (N) of a protein than to the unfolded state (U). Show that the ligand stabilizes the protein and calculate by how much (ΔΔGfold = ?). Please help me find out deltadelta G fold.
Which of the following statements about protein folding and structure are true? Check all that apply. Chaperones, like the GroEL-ES complex, work by providing a sequestered environment in which proteins can safely explore the conformational space towards productive folding. O Chaperones "know" how to actively fold proteins into their proper final structure. Each protein has its own "assigned" chaperone to assist in its proper folding. O Misfolded proteins are innocuous and readily cleared by the cell. V The native structure of a protein is entirely encoded in its amino acid sequence. Misfolded proteins often aggregate in large structures in the cell. Misfolded proteins are thermodynamically stable versions of a protein.
. Theoretical and experimental measurements show that in many cases, the contributions of ionic and hydrogen-bonding interactions to AH for protein folding are close to zero. Provide an explanation for this result.,
4. a. Give the full names of the amino acids in this peptide. НзN — CH—С-N—CH— С-N—CH—С—О ČH3 H ČH,OH H. CH2 -ОН b. Calculate the isoelectric point (pl) of a peptide with sequence SNARE. Show your work in a table, giving the pKa values of the ionizable groups, pH, and charges. Step marks are counted. Don't need to write “protonated" or “deprotonated".
3. Amino Acid Sequence and Protein Structure Our growing understanding of how proteins fold allows researchers to make predictions about protein structure based on primary amino acid sequence data. Consider the following amino acid sequence. 1 3 5 6 7 8 9 10 Ile - Ala - His - Thr - Tyr - Gly - Pro - Phe-Glu – Ala- - 11 12 13 14 15 17 20 Ala - Mat - Cys- Lys - Trp - Glu-Ala-Gln-Pro - Asp- 16 18 19 21 22 23 24 25 26 27 28 Gly - Met-Glu - Cys - Ala - Phe - His - Arg (a) Where might bends or ß turns occur? (b) Where might intrachain disulfide cross-linkages be formed? (c) Assuming that this sequence is part of a larger globular protein, indicate the probable location (external surface or interior of the protein) of the following amino acid residues: Asp, lle, Thr, Ala, Gln, Lys. Explain your reasoning.
Which of the following amino acids are more likely to be on the interior of the protein? And which are more likely to be exposed to the surface? L I D E W A V K H M Q Y
4. Deducing quaternary structure via SDS-PAGE. SDS-PAGE is a convenient method for separating polypeptides solely on the basis of size. Small polypeptides travel faster than large ones; rate of migration through the gel is inversely proportional to the logarithm of molecular weight. The subunit structure of a multimeric protein often can be deduced using this technique in conjunction with a protein cross-linking agent. Cross-linking agents react with amino acid residues of two polypeptides that are in contact, thereby linking them by covalent bonds. After limited treatment with the reagent, so that some but not all subunits become cross-linked to their neighbors, the protein is subjected to SDS-PAGE and the molecular weights of the resulting proteins (bands) are estimated. The results of such experiments on two proteins (Protein A and Protein B) are shown below. What is the most likely subunit structure of each protein? Protein A SDS-PAGE cross-linking agent MW 105,000 70,000 35,000…
N. HN H3N Where on this amino acid does it attach to a primary sequence of a protein and where is the ionizable position of the R group?
. A protein has been sequenced after cleavage of disulfide bonds. The protein is known to contain 3 Cys residues, located as shown below. Only one of the Cys has a free - SH group and the other two are involved in an -s-s- bond. A Phe Cys « N-terminus Cys- - Met Cys- C-terminus The only methionine and the only aromatic amino acid (Phe) in this protein are in the positions indicated. Cleavage of the intact protein (i.e., with disulfide bonds intact) by either cyanogen bromide or chymotrypsin does not break the protein into two peptides. Where is the -s-s- bond (i.e., AB, BC, or AC)?
Long-range interactions between residues on a single polypeptide chain are classified as quaternary structures. On the other hand, interactions between residues on separate polypeptide chains are classified as tertiary structures. O Both statements are correct O The first statement is correct while the second statement is incorrect O Both statements are incorrect O The first statement is incorrect while the second statement is correct