1. Amino acid side chains act as nucleophiles and proton donor/acceptors in various enzymaticreactions. We will use them frequently in reactions during 40B and therefore the purpose of thisexercise is to review the properties of amino acid side chains you have learned in 40A.Ozempic is a medication used for the treatment of type 2 diabetes and an anti-obesity treatment.Ozempic is a modified peptide that mimics the structure of the natural hormone GLP-1.H-His-N GAU-GH₂C CH₂Glu-Gly-Thr-Phe-Thr-Ser Asp-Val-Ser-Ser-Tyr-Leu-Glu-Gly Gin-Ala-Ala-a.NHH-His-noH₂C CH₂au PhoPhe-lle Ala Trp Leu-Val-Arg Gly Arg-Gly-OHAdd above the tree-letter code of each amino acid the relevant functional group on its side chain.OHIFor example: -Ser- will be represented by SerNHOHb. The protonation state of each functional group depends on the pH of the solution. Assume thatOzempic is in a solution at pH=7. Draw the functional groups at their correct protonation form.Gu-GyGlu-Gy-Thr-Phe-Thr-Ser-Asp-Val-Ser-Ser-Tyr-Leu-Glu-Gly-Gin-Ala-Ala-Gu Phe-Phe-lle Ala-Trp Leu-Val-Arg-Gly-Arg-Gly-OHOHC. What will be the protonation state of the long non-peptide side chain at pH=7?

Ozempic works like a little coach for your body, helping fight high blood sugar in type 2 diabetes.…

Answered: 1. Amino acid side chains act as…

Biochemistry

9th Edition

ISBN:9781319114671

Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Chapter1: Biochemistry: An Evolving Science

Section: Chapter Questions

Problem 1P

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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
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…
1. Amino acid side chains act as nucleophiles and proton donor/acceptors in various enzymatic reactions. We will use them frequently in reactions during 40B and therefore the purpose of this exercise is to review the properties of amino acid side chains you have learned in 40A. Ozempic is a medication used for the treatment of type 2 diabetes and an anti-obesity treatment. Ozempic is a modified peptide that mimics the structure of the natural hormone GLP-1. a. Gay-The Phe-The-Ser Asp-Val-Ser-Ser-Tyr-Leu-Glu-Gily Gin-Ala-Ala-auhe-s NH C. For example: -Ser- will be represented by Gu Phe-lle Ala-Trp -Leu-Val-Arg-Gly Arg Gly-OH Add above the tree-letter code of each amino acid the relevant functional group on its side chain. OH Ser The protonation state of each functional group depends on the pH of the solution. Assume that Ozempic is in a solution at pH=7. Draw the functional groups at their correct protonation form. O Gu Phe-le- Ala-Trp Leu-Val- Arg-Gly Arg-Gly-OH Quay Thr Phe Thr-Ser…
4.1
3. Triose-phosphate isomerase (TPI) catalyzes the movement of a single proton to interconvert dihy- droxyacetone phosphate and glyceraldehyde 3-phosphate in glycolysis and gluconeogenesis. The enzyme, a dimer of identical subunits that are 248 amino acids in humans, has no cofactors, required metal ions, or cooperativity between subunits. The enzyme is found in all tissues. The value of Kcat/KM - 9.2 x 106 sec-'M-1 is close to the rate constant expected for a diffusion-limited reaction. The mechanism of the proton transfer is illustrated in the diagram below. Glu-165 Giu-165 Glu-165 ks HR H 20,PO HO, OH His-95 His-95 His-95 (a) ing structural formulas and naming enzymes and glycolytic intermediates, the reactions of the payoff phase. Consider only anerobic glycolysis. Remember that each glucose molecule yields two mole- cules of glyceraldehyde-3-phosphate (GAP). Indicate the net yield of ATP and NADH generated through anaerobic glycolysis per glucose molecule. The reaction catalyzed by…
If phenylalanine was not an essential amino acid, would diet therapy (the elimination of phenylalanine from the diet) for PKU work? Do not just say yes or no. Give a short explanation for this hypothetical situation.
5
IX. Insulin, a hormone vital in blood sugar regulation and having a polypeptide chain with disulfide linkages, loses its regulatory activity when heated at nearly 100°C for 5-10 minutes. Explain the molecular basis of this observed thermal property of insulin relative to its native structure and function. I--
H CH₂ H₂C HC-CH3 CH₂ H H₂C (S) H₂C H CH₂ CH₂ CH₂ NH O C NH NH₂ a) Which of the following statements about this peptide are correct? Group of answer choices Treatment of this peptide with trypsin generates two products. This peptide is a substrate for carboxypeptidase A Treatment of this peptide with cyanogen bromide generates a pentapeptide and a tripeptide. Treatment of this peptide with chymotrypsin generates three products. Treatment of this peptide with elastase generates 2 products. None of the above statements are correct. b) What is the sequence of this peptide using one letter abbreviations? c) What is the pH which would correspond to the ionization of the peptide as drawn above? 1, 5, 7, 10, 14
In class, I mentioned that fructose is metabolized differently in the liver compared to glucose. Refer to the figure shown below to calculate the number ofATPs you would expect from the metabolism of fructose in the liver. Show your work! Fructokinase Fructose Fructose-1-P АТР ADP Aldolase B Dihydroxy- acetone phosphate Glyceraldehyde АТР Triose kinase Triose phosphate isomerase ADP 4 - Glyceraldehyde-3-P Glycolysis Руruvate Acetyl-CoA Fatty acids and triglycerides
E Threonine 6. You have identified some intermediates in threonine synthesis: A, B, C, D and E. You grow a few of your mutants in the presence of these different intermediates to determine the order in which the gene products act. Below are your results. A (+) means growth and a (-) means no growth. Given these data, draw the best possible pathway for the synthesis of threonine. The diagram should use arrows to indicate one intermediate being changed to another intermediate. Indicate which gene produces the product responsible for the conversion by listing the mutant in that gene above the arrow. Mt1 Mt2 Mt4 Mt7
One of the reasons for oxidizing the disulfide bonds in RNase A before removing the urea in the Anfinsen experiment was to demonstrate that ... Urea promotes disulfide bond exchange O Incorrectly-folded proteins lose their enzymatic activity. Urea prevents disulfide bond formation. Urea forms thio-esters with reduced cysteines at pH 8.2 Disulfide bonds are required for enzyme activity.

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