5. Protein folding is largely influenced by the interaction of the R-groups (side chains) with theenvironment. Explain how this interaction relates to the polarity of the R-groups. How does thefact that the proteins must fold in certain ways because of these interactions affect the number ofconfigurations available to the protein?6. We also have to think about entropic factors when we think about thermodynamic stability.Entropic factors influence the number of different configurations in which submicroscopiccomponents of the substance may exist. Think about your answer to question 5 - Does proteinfolding increase or decrease entropy? Justify your answer.2. Sketch a simple picture of both a folded and an unfolded protein. This can be represented as just aline.a. Thinking about your answer to question number one, which configuration do you expect tobe preferred? Justify your answer.

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5. Protein folding is largely influenced by the interaction of the R-groups (side chains) with the environment. Explain how this interaction relates to the polarity of the R-groups. How does the fact that the proteins must fold in certain ways because of these interactions affect the number of configurations available to the protein?

5. Protein folding is largely influenced by the interaction of the R-groups (side chains) with the environment. Explain how this interaction relates to the polarity of the R-groups. How does the fact that the proteins must fold in certain ways because of these interactions affect the number of configurations available to the protein?

Biology: The Dynamic Science (MindTap Course List)

4th Edition

ISBN:9781305389892

Author:Peter J. Russell, Paul E. Hertz, Beverly McMillan

Publisher:Peter J. Russell, Paul E. Hertz, Beverly McMillan

Chapter6: Energy, Enzymes, And Biological Reactions

Section: Chapter Questions

Problem 9TYK: Which of the following statements about inhibition is true? a. Allosteric inhibitors and allosteric...

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1. The use of natural proteins as drugs requires compliance with certain storage and use conditions, which are clearly prescribed in the instructions. So, most protein preparations must be stored in a refrigerator at a temperature not excce- ding 10 °C, and dry preparations should be dissolved in boiled water cooled to room temperature. Some protein preparations are stored in hermetically scaled ampoules, from which air is removed. Why do protein drugs require strict adherence to all the conditions prescribed in the instructions, and what can happen if these conditions are violated?
5. Consider the reaction for assembly of a tetrapeptide from for amino acids: Serine + Proline + Alanine + Methionine ----> SPAM tetrapeptide Is this reaction anabolic or catabolic? Is this a positive or negative delta G reaction? List at least three other terms you could use to describe this reaction. 6. Consider the reaction: Glutamic acid + Ammonia + ATP ----> Glutamate + ADP + Pi Is this reaction anabolic or catabolic? Is this a positive or negative delta G reaction? This is actually an example of a coupled reaction! Briefly, explain why reaction coupling is required, and how it works in this example.
4. Consider the amino acid aspartic acid for this problem. Aspartic acid can be considered a triprotic acid with three ionizable protons with pka's of 1.99, 3.90, and 9.90. When fully protonated aspartic acid has a charge of +1. a. Sketch the titration curve of aspartic acid from pH values of 0.0 to 14.0 below. b. Suppose you began your titration with 10.0 mM aspartic acid. Complete the following concentration table as a function of pH (the first row is "-1" species "-2" species + provided to help you get started): pH 0.0 1.99 2.99 9.90 10.90 "+1" species "0" (neutral species) 0 10.0 mM 0 c. Calculate the isoelectric point of aspartic acid: 0 d. At what pH do you think aspartic acid is least soluble? Explain briefly.
7. Consider the role of energetic and entropic factors for protein folding. a. Draw a PEC diagram that represents the relative potential energy and number of configurations for the unfolded and folded protein.
1. Consider the three-dimensional model of the tertiary structure of an enzyme below. Amino acids involved in binding are shaded blue, and amino acids involved in catalysis are shaded red. A. Suppose research has shown that amino acid 82 in the red shaded region is lysine, an amino acid with a positively-charged side chain. This lysine is critical for catalysis. Other studies have found that amino acids 12 and 62 in the blue region are both phenylalanine, an amino acid with a nonpolar side chain, and are critical for substrate binding. These amino acids are relatively close in the active site but are separated by 20-70 amino acids in the primary structure. Using what you know about protein structure, explain how amino acids separated in the primary structure can come close together in the active site. B. Use this information and figure 4.2 in your book to answer the following questions: Do you think changing amino acid 82, lysine, an amino acid with a positively-charged side…
2. Cofactors, coenzymes, and prosthetic groups are important non-protein substances that are required for enzyme function. This is a table of cofactors/coenzymes/prosthetic group we've discussed. Draw the functional portion of the cofactor/pro and explain the functional role in each reaction. a. Cofactor Name thiamine pyrophosphate (TPP) oxidized Lipoamide/lipoic acid/lipoyl-lysine Coenzyme A (CoASH) flavin adenine dinucleotide (FAD) reduced nicotinamide adenine dinucleotide (NADH + H+) oxidized nicotinamide adenine dinucleotide (NADP+) biotin Reaction Pyruvate -> acetaldehyde Pyruvate -> Acetyl CoA aKetoglutarate -> Succinyl-CoA Succinate -> Fumarate Pyruvate -> lactate 6-Phosphogluconate -> Ribulose 5- phosphate Bicarbonate + pyruvate -> oxaloacetate Structure of only the cofactor Functional or catalytic role
4) Explain the physical implications of the following diagram: ENERGY vum им Intermediate folding states m W Folded protein W CONFIGURATION Figure 1: The Thermodynamics of Protein Unfolding²
11. Below is a folding energy funnel describing folding energy landscape of a protein. The width of the funnel 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 molten globule? How does this state differ from A in term of structures. B) Does this protein have multiple folding pathways or just one? C) which state has the lowest free energy? D) According to the width of the funnel, the native state B of the protein has the lowest entropy. If the protein fold A spontaneously to this state, does it violate the 2nd law of thermodynamics? Why or why not? (Hint: in the 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 the protein folds? 12. List four methods by which a protein can be denatured and briefly describe how these methods act to disrupt protein structure.
16. A quantitative study of the interaction of a protein with its ligand yielded the following results: Ligand concentration 0.5 1 2 3 4 5 6 9. 12 (μM) v (moles of 0.14 0.31 0.48 0.61 0.68 0.72 0.77 0.79 0.81 ligand bound per mole of protein) Plot a graph of ligand concentration versus v. Determine KD, the dissociation constant for the interaction between the protein and its ligand, from the graph.
3. Solve the sequence of an oligopeptide 7 residues long which gave: Asp Leu Lys Met Phe Tyr The following facts were observed: a. Trypsin treatment had no apparent effect b. The PTH derivative from Edman degradation was c. Brief chymotrypsin treatment yielded several products including but not limited to a dipeptide and a tetrapeptide. The amino acid composition of the tetrapeptide was Leu, Lys, and Met. d. Cyanogen bromide treatment yielded a dipeptide, a tetrapeptide, and a free Lys.
1. 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 (DDGfold = ?) 2. An enzyme E binds a substrate S and a cofactor C. The equilibrium dissociation constant Kd,S of the enzyme-substrate complex ES is 1 μM, for EC it is 10 μM. When the cofactor C is present, Kd,s’ is decreased to 0.1 μM. What is the value for the dissociation constant Kd,C’ of the enzyme-cofactor complexing the presence of substrate S? Calculate the interaction energy DDGint for cofactor and substrate binding.
1. In the mechanism of action of triose phosphate isomerase, Lys12 is an essential amino acid in the flexible phosphate gripper loop that undergoes a large conformational change to trap the substrate in the active site excluding water and holding the phosphate group in the correct geometry for isomerization rather than dephosphorylation. What would be the effect of the mutation of Lys12 to the unusual amino acid shown below? Explain. protein backbone