Biochemistry
6th Edition
ISBN: 9781305577206
Author: Reginald H. Garrett, Charles M. Grisham
Publisher: Cengage Learning
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Chapter 6, Problem 16P
Answers to all problems are at the end of this book. Detailed solutions are available in the Student Solutions Manual, Study Guide, and Problems Book.
(Research Problem) Conformational Transitions in Proteins How do proteins accomplish conformational changes? How is it that proteins convert precisely and efficiently from one conformation to another'.’ Recall from Figure 6.54 that any folding/unfolding transition must involve movement across a free-energy landscape, and try to imagine the nature of a conformational transition. Are bonds formed and broken along the way'.' What kinds of bonds and interactions might be involved? Suggest how such conformational transitions might occur. One reference that will be useful in this regard is:
Boehr. D.. 2009. During transitions proteins make fleeting bonds. Cell 139: 1049-1051.
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Chapter 6 Solutions
Biochemistry
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- Answers to all problems are at the end of this book. Detailed solutions are available in the Student Solutions Manual, Study Guide, and Problems Book. (Research Problem) The Nature and Roles of Linear Motifs in Proteins In addition to domains and modules, there are other significant sequence patterns in proteins—known as linear motifs—that are associated with a particular function. Consult the biochemical literature to answer the following questions: 1. What are linear motifs? 2. How are they different from domains?. 3. What are their functions? 4. How can they be characterized? 5. There are several papers that are good starting points for this problem. Neduva, V., and Russell, R., 2005. Linear motifs: evolutionary interaction switches. FEBS Letters 579:3342-3345. Gibson, T., 2009. Cell regulation: determined to signal discrete cooperation. Trends in Biochemical Sciences 34:471-482. Diella, K. Haslam, N., Chica., C. et aL, 2009. Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Frontiers of Bioscience 13:6580-6603.arrow_forwardAnswers to all problems are at the end of this book. Detailed solutions are available in the Student Solutions Manual, Study Guide, and Problems Book. To fully appreciate the elements of secondary structure in proteins, it is useful to have a practical sense of their structures. On a piece of paper, draw a simple but large zigzag pattern to represent a -strand. Then fill in the structure, drawing the locations of the moms of the chain on this zigzag pattern. Then draw a simple, large coil on a piece of paper to represent an -helix. Then fill in the structure, drawing the backbone atoms in the correction locations along the coil and indicating the locations of the R groups in your drawing.arrow_forwardAnswers to all problems are at the end of this book. Detailed solutions are available in the Student Solutions Manual, Study Guide, and Problems Book. Evaluation of -Helices in Proteins The hem agglutinin protein in influenza virus contains a remarkably long -helix, with 53 residues. How long is this -helix (in nm)? How many turns does this helix have? The typical residue in an -helix is involved in two H bonds. How many H bonds are present in this helix?arrow_forward
- Answers to all problems are at the end of this book. Detailed solutions are available in the Student Solutions Manual, Study Guide, and Problems Book. (Research Problem) The Nature of Protein-Protein Interactions How do proteins interact? When one protein binds to another, one or both changes conformation. Two hypotheses have been proposed to describe such binding: In the induced fit model, the interaction between a protein and a ligand induces a conformation change (in the protein or ligand) through a step wise process. In the conformational selection model, the unliganded protein (in the absence of the ligand) exists as an ensemble of conformations in a dynamic equilibrium. The binding ligand interacts preferentially with one among many of these conformations and shifts the equilibrium in favor of the selected conformation. Three recent papers shed light on this question: Boehr, D.. and Wright, P. E., 2008. How do proteins interact? Science 320:1429-1430. Gsponer, J.. et al., 200&. A coupled equilibrium shift mechanism in calmodulin-mediated signal transduction. Structure 16:736—'746. Lange, O., et al., 2008. Recognition dynamics up to microseconds revealed from an R DC-derived ubiquitin ensemble in solution. Science 320:1471-1475. Consult these papers and answer the following questions: What proteins were studied in these papers? What techniques were used, and what time scales of protein motion were studied? What were the conclusions of these papers, and how do these results illuminate the choice between induced fit and conformational selection in protein-protein interactions?arrow_forwardAnswers to all problems are at the end of this book. Detailed solutions are available in the Student Solutions Manual, Study Guide, and Problems Book. Solving the Sequence of an Oligopeptide From Sequence Analysis Data Amino acid analysis of ail oligopeptide seven residues long gave The following fads were observed: a. Trypsin treatment had no apparent effect. b. The phenylthiohydantoin released by Lid mini degradation was c. Brief chymotrypsin treatment yielded several products, including a dipeptide and a tetrapeptide. The amino acid composition of the tetrapeptide was Leu, Lyi. and Met. d. Cyanogen bromide treatment yielded a dipeptide, a tetrapeptide, and free Lys. What is the amino acid sequence of this heptapeptide?arrow_forwardAnswers to all problems are at the end of this book. Detailed solutions are available in the Student Solutions Manual, Study Guide, and Problems Book. The Role of Proline Residues in -Turns Pro is the amino acid least commonly found in «-helices but most commonly found in -turns. Discuss the reasons for this behavior.arrow_forward
- Answers to all problems are at the end of this book. Detailed solutions are available in the Student Solutions Manual, Study Guide, and Problems Book. Consider a protein that can exist in two forms: folded and unfolded. Calculate the free energy difference at 298 k. between a state in which SU% of the protein is folded and a state in which 80%of the protein is unfolded.arrow_forwardAnswers to all problems are at the end of this book. Detailed solutions are available in the Student Solutions Manual, Study Guide, and Problems Book. A Rule of Thumb for Amino Acid Content in Proteins The simple average molecular weight of the 20 common amino adds is 138, but most biochemists use 110 when estimating the number of amino acids in a protein of known molecular weight. Why do you Suppose this is? (Hint: There are two contributing factors to the answer. One of them will be apparent from a brief consideration of the amino acid compositions of common proteins. See, for example, Figure 5.16 of this text.)arrow_forwardAnswers to all problems are at the end of this book. Detailed solutions are available in the Student Solutions Manual, Study Guide, and Problems Book. Assessing the Roles of Weak Forces Between Amino Acids in Proteins Discuss the potential contributions to hydrophobic and van der Waals interactions and ionic and hydrogen bonds for the side chains of Asp, Leu, Tyr and His in a protein.arrow_forward
- Answers to all problems are at the end of this book. Detailed solutions are available in the Student Solutions Manual, Study Guide, and Problems Book. Solving the Sequence of an Oligopeptide From Sequence Analysis Data Amino acid analysis of a decapeptide revealed the presence of the following products: The following facts were observed: Neither car boxy peptidase A nor B treatment of the- decapeptide had any effect. Trypsin treatment yielded two tetrapcptides and free Lys. Clostripain treatment yielded a tetrapcptide and a hexapeptidc. Cyanogen bromide treatment yielded an octapeptide and a dipeptide of sequence NP (using the one-letter codes). Chymotrypsin treatment yielded two tripeptides and a telrapeptide. The N-terminal chymotryptic peptide had a net charge of — 1 at neutral pi I and a net charge of —3 al pH 12. One cycle of Ed man degradation gave the PTH derivative What is the ammo acid sequence of this decapeptide?arrow_forwardAnswers to all problems are at the end of this book. Detailed solutions are available in the Student Solutions Manual, Study Guide, and Problems Book. Solving the Sequence of an Oligopeptide From Sequence Analysis Data Amino acid analysis of an oligopeptide containing nine residues revealed the presence of the following amino adds: Arg Cys Gly Leu Met Pro Tyr Val The following was found: Carboxypeptidase A treatment yielded no free amino add. Edman analysis of the intact oligopeptide released c. Neither trypsin nor ehymotrypsin treatment of the nonapeptide released smaller fragments. However, combined trypsin and chymotrypsin treatment liberated free Arg. CNBr treatment of the eight-residue fragment left after combined trypsin and chymotrypsin action yielded a six-residue fragment containing Cys* Gly. Pro, Tyr, and Val and a dipeptide. Treatment of the six-residue fragment with -mercaptoethanol yielded two tripeptidcs. Brief Edman analysis of the tripeplide mixture yielded only Ρ�Ή-Cys. (The sequence of each tripeptide, as read from the N-terminal end, is alphabetical if the one-lelter designation for amino acids is used.) What is the amino acid sequence of this nonapeptide?arrow_forwardAnswers to all problems are at the end of this book. Detailed solutions are available in the Student Solutions Manual, Study Guide, and Problems book. Understanding the Role of Gly Residues In Protein Secondary and Tertiary Structure It is often observed that Gly residues are conserved in proteins to a greater degree than other amino acids. From what you have learned in this chapter, suggest a reason for this observation.arrow_forward
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