Biological Science (6th Edition)
6th Edition
ISBN: 9780321976499
Author: Scott Freeman, Kim Quillin, Lizabeth Allison, Michael Black, Emily Taylor, Greg Podgorski, Jeff Carmichael
Publisher: PEARSON
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Chapter 3, Problem 6TYU
Summary Introduction
To review:
The mechanism used by molecular chaperones to facilitate protein folding in many different polypeptides, each with their own specific shape.
Introduction:
The molecular chaperones are a large family of highly conserved proteins that help in covalent folding or unfolding of proteins.
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The amide hydrogen atoms of peptide bonds within proteins can exchange with protons in the solvent. In general, amide hydrogen atoms in buried regions of proteins and protein complexes exchange more slowly than those on the solvent-accessible surface do. Determination of these rates can be used to explore the proteinfolding reaction, probe the tertiary structure of proteins, and identify the regions of protein–protein interfaces. These exchange reactions can be followed by studying the behavior of the protein in solvent that has been labeled with deuterium ( ²H), a stable isotope of hydrogen. What two methods described in this chapter could be readily applied to the study of hydrogen– deuterium exchange rates in proteins?
Which of the following statements are true?
Electrostatic interactions are the dominant forces in protein molecular recognition.
When two proteins form a complex there is an unfavorable loss of rotational-translational entropy.
Protein-protein interfaces are most often dry. The exclusion of water results in an unfavorable loss in rotational-translational entropy.
The free energy change associated with the formation of an enzyme-substrate complex almost always results in an unfavorable reduction in conformational entropy of the proteins.
Burial of an uncompensated positive charge inside proteins is usually unfavorable.
So-called van der Waals’ interactions are essentially electrostatic in origin.
Steric complementarity of the two partners forming a complex is essential to achieve optimal free energy of binding.
Structural models of proteins obtained from low temperature crystallography are excellent descriptions of all biochemically relevant aspects of their function.
list other biological examples in which specific protein interactions are involved.
Chapter 3 Solutions
Biological Science (6th Edition)
Ch. 3 - 1. What two functional groups are bound to the...Ch. 3 - 2. What type of bond is directly involved in the...Ch. 3 - What type of information is used to direct...Ch. 3 - 4. What is an active site?
a. the location in an...Ch. 3 - Prob. 5TYUCh. 3 - Prob. 6TYUCh. 3 - 7. Why are proteins not considered to be a good...Ch. 3 - Prob. 8TYUCh. 3 - Prob. 9TYPSSCh. 3 - 10. Make a concept map (see BioSkills 12) that...
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- Consider protein folding that results when the following components interact: Where the solution is at a pH of 7, green (thick-dotted line) represents aspartic acid (R group contains a carboxylic acid with pKa = 4), orange (thick-solid line) represents lysine (R group contains an amine with pKa = 10), and blue (thin-solid line) represents hydrophilic groups. Rank the three complexes in order from lowest to highest dissociation constants Kd (low Kd values correspond to good binding constants and low energy, while high Kd values correspond to low binding constants and high energy) as determined by intermolecular charge-charge interactions. For those complexes with charge-charge interactions being equal, look at the possibility for the formation of hydrogen bonds via carboxylic acid dimers (only possible when the carboxylic acid is protonated) which are low energy structures.arrow_forwardConsider the following in light of the concept of levels of structure (primary, secondary, tertiary, quaternary)as defined for proteins.(a) What level is shown by double-stranded DNA?(b) What level is shown by tRNA?(c) What level is shown by mRNA?arrow_forwardConsider the following in light of the concept of levels of structure (primary, secondary, tertiary, quaternary) as defined for proteins. (a) What level is shown by doublestranded DNA? (b) What level is shown by tRNA? (c) What level is shown by mRNA?arrow_forward
- You've isolated a novel protein, but you believe what you actually have is a mixture of the unmodified and phosphorylated protein. Which of these methods would be best for helping you to determine if you do indeed have a mixture of phosphorylated and non-phosphorylated protein, while also establishing other vital characteristics of this novel protein? O 2D-PAGE O SDS-PAGE O Isoelectric focusing O Native-PAGEarrow_forwardProper folding of proteins is essential for their biological activity. In general, the functional conformation of a protein is the conformation with lowest energy. This means that if an unfolded protein is allowed to reach equilibrium, it should assemble automatically into its native, functioningfolded state. Why then is there a need for molecular chaperones and chaperonins in cells? What different roles do molecular chaperones and chaperonins play in the folding of proteins?arrow_forwarda. 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'arrow_forward
- Consider 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_forwardDescribe the general structure of a type 2 alpha helix protein. Explain how type 2 alpha helix transmembrane domains can be used to form pathways for large polar and charged molecules to traverse the lipid bilayer of the cell membrane.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). Do only part B.arrow_forward
- The amide hydrogen atoms of peptide bonds within proteins can exchange with protons in a solvent. In general, amide hydrogen atoms in buried regions of proteins and protein complexes exchange more slowly than those on the solvent-accessible surface. By determining these exchange rates, we can explore protein-folding reactions, probe the tertiary structure of proteins, and identify the regions of protein-protein interfaces. We can investigate these exchange reactions by studying the behavior of the protein in solvent that has been labeled with deuterium, 2H, a stable isotope of hydrogen. Select the methods that could be readily applied to the study of hydrogen-deuterium exchange rates in proteins. enzyme-linked immunosorbent assay (ELISA) nuclear magnetic resonance (NMR) spectroscopy x-ray crystallography mass spectrometry (MS)arrow_forwardNon covalent bonds are very important in cell biology, could you explain why and provide an example that illustrates their importance ( do not chose protein folding as an example) What are the different levels of protein structure and what are the different parameters (sequence, type of bonds, etc...) that influence protein folding at these different levels?arrow_forwardConsider the following peptide to answer the questions below: A M A K K E S H I F T A I D E What is the total charge of this peptide at pH = 5? What is the N terminal amino acid (full name)? C terminal amino acid? How many fragments would result if this peptide underwent proteolytic cleavage with V-8 protease and what are these fragments (list them)? Would this peptide be a candidate to form an alpha helix? Why or why notarrow_forward
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Biomolecules - Protein - Amino acids; Author: Tutorials Point (India) Ltd.;https://www.youtube.com/watch?v=ySNVPDHJ0ek;License: Standard YouTube License, CC-BY