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- 4. a. Calculate the KM (Michaelis constant) and the vmax (the maximum initial rate) for both substrates (sphingosine and ATP). Show your work, and be careful about units. b. threo-dihydrosphingosine, a stereoisomer of sphingosine, is an inhibitor of sphingosine kinase. What kind of inhibitor (competitive, uncompetitive, noncompetitive) is threo-dihydrosphingosine? Citing information from the Lineweaver-Burke plots, explain how you can tell.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…a. Protein X can be phosphorylated. Why would the phosphorylated form of protein X elute AFTER the unphosphorylated form from an ANION exchange column? Please describe in terms of: The chemical properties of phosphorylation modification b. The chemical properties of an anion exchange column and how it works c. Why is an inhibitor that mimics the transition state more effective at enzyme inhibition than an inhibitor that mimics the substrate? d. Protein X can be covalently modified with many methyl groups. What two general properties would be different between the unmethylated protein versus the methylated protein?
- 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.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 role8.Choose the False statement about enzyme binding sites Binding at an allosteric site ca affect binding and catalysis at the Ortho steric site. In addition to ortho steric sites , some enzymes have other sites where catalysis can be conducted. They are called , allosteric sites, from “allo,” the other. In principle, allosteric ligands can have structures that do not resemble those of substrates. Ligand binding at an allosteric site can cause a conformational change of an enzyme. Enzyme can be inhibited by an allosteric ligand that does not complete with substrate.
- 1. If a molecule is interating with its side chains of an enzymes active site but it is not the substrate of the enzyme what kind of enzyme regulation is this? 2. What is the change in thetype of bond between Ser 80 -> Arg. 3. Will this change cause the complex to be more or less stable. Explain1 ).Which of the following accurately describes substrate specificity for serine proteases? A.The binding cleft B.Mg2+ metal activated enzyme C.The catalytic triad D.Facilitates redox chemistry E.Stabilizes the transition state 2). Which of the following amino acid residues would not provide a side chain for acid-base catalysis at physiological pH? select all that apply leucine aspartic acid histidine lysine Please answer both correct i will give u upvote.A7. Consider what can be concluded about the catalytic site (substrate binding site) of phosphatase and the binding site of NaF from the type of inhibition shown by NaF for phosphatase and illustrate it schematically. The inhibition typre is pure noncompetitive inhibition.
- 3. MUTPase from ASFV (aDUT) and from swine (listed as sDUT) were studied in the absence and present of the DUTP substrate. Using the melting temperature data provided below, how does adding the substrate affect enzyme stability? Explain your choice in 25 words or less. TemperatureL°CT protein Tm by thermal denaturation (°C) aDUT 83.1 ± 0.2 SDUT 61.8 + 0.2 aDUT-DUTP-Mg SDUT-dUTP-Mg 84.5 + 0.1 62.7 + 0.2 a. The substrate makes aDUT less stable and SDUT more stable b. The substrate makes aDUT more stable and $DUT less stable c. The substrate makes both ADUT and SDUT less stable d. The substrate makes both aDUT and SDUT more stable sh (United States) D. Focus rch 7:15 80°F ENG 7/10/2 DELL F3 F4Below is a plot of Vo vs. [S] for a specific allosteric enzyme under different conditions. Which of the following best describes the graph? 4 (S] O Adding a positive modulator to #2 would result in curve 3. Curve 1 represents maximum inhibition. Line 4 is valid exclusively for curves 1 and 2. Adding a positive modulator to #1 would result in curve 2. O Curve 3 represents the effect of a negative modulator added to curve 2.On the graph provided, sketch a plot of Vo/Vmax vs. [S] for an allosteric enzyme, 1.0 0.8 0.6 0.4 02 [Substrate] A. in the absence of any other ligand besides the substrate B. in the presence of an allosteric inhibitor C. in the presence of an allosteric activator. Clearly LABEL the 3 curves A, B and C