3. (Part A) The intermediates of a pathway are shown in the following scheme. Using curvedarrows, show the mechanism of each step labeled with a blue letter. Draw out the structures ofall coenzymes, so that you can effectively show all arrow pushing. You may abbreviate thecoenzymes by putting R groups on the molecule, but do draw out the parts of the structure thatare involved in the arrow pushing.Please note that some of the transformations will require you to show multiple structures toshow all of the arrow pushing (particularly some of the coenzyme-mediated steps). You do notneed to show specific amino acid residues that perform the catalysis. You can abbreviate acidicamino acid residues "Enz-B-H" and basic residues "B-Enz".HOOOHONH₂OHATP ADP(A)H₂O3POH₂O(D)O NH₂OHO.OOHNADPH(B)NADP+OHILI I IgrOHHOOHO OH NH₂O NH₂H₂OOH(E)(C)OHOH

The metabolic pathway in question involves the conversion of the amino acid aspartate to chelidamic…

Answered: (Part A) The intermediates of a pathway…

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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Intermediates of a pathway are shown in the following scheme. Using curved arrows, show the mechanism of each step labeled with a blue letter. Draw out abbreviated structures of the coenzymes, so that you can effectively show all arrow pushing. You may abbreviate the coenzymes by putting R groups on the molecule, but do draw out the parts of the structure that are involved in the arrow pushing. Some of the transformations will require you to show multiple structures to show all of the arrow pushing (particularly some of the coenzyme-mediated steps). You do not need to show specific amino acid residues that perform the catalysis. You can abbreviate acidic amino acid residues “Enz–B–H” and basic residues “B–Enz”.
1. Provide the best coenzyme(s) for each step shown below. Give a 1–2 sentence rationale for your choice. 2. Reaction (C) can require multiple coenzymes, or the enzyme may only require one. Briefly describe how the reaction that uses only one coenzyme works. Be specific about the mechanism.
The highest energy point of the serine protease reaction is the formation of the tetrahedral oxyanion intermediate on the original carbonyl carbon of the scissile peptide bond. True or False? DIPF is an irreversible inhibitor of serine proteases. True or False? The acyl-enzyme intermediate is the transition state of the reaction. True or False? Serine proteases are classified as isomerases. True or False?
The products of a pathway, or the products of specific reactions in the pathway, will often inhibit upstream regulatory enzymes in that pathway. That makes sense - if the products of a pathway are abundant, then the pathway can be shut off to save energy or divert molecules into other pathways. We can use a similar rule of thumb to predict whether a pathway will be active in different biological states. For example, the liver stores glucose (in the form of glycogen), and will release glucose into the bloodstream when blood sugar levels drop. This glucose can come from the synthesis of glucose or breakdown of stored glycogen. This is important for maintaining blood sugar levels. What would you predict is the relationship between blood sugar levels and glycogen phosphorylase enzyme activity? A positive relationship (when blood sugar levels are high, glycogen phosphorylase activity is also high). A negative relationship (when blood sugar levels are high, glycogen phosphorylase activity…
For each step of the citric acid cycle, name the enzyme responsible for the chemical transformation that occurs and classify the enzyme type: Step 1. Step 2. Step 3. Step 4. Step 5. Step 6. Step 7. Step 8. i. oxidoreductase (oxidases, reductases, dehydrogenases) ii. transferase (transaminases, kinses) iii. hydrolase (lipases, proteases, nucleases, carbohydrases, phosphateses) iv. lyase (dehydratase, decarboxylase, deaminase, hydratase) v. isomerase (racemases, mutases) vi. ligase (synthetases, carboxylaces) Enzyme Name Enzyme Type
Match the following catalytic strategies with their example. Place a Letter on the picture. There are only two examples given. CH2OH CH2OH CH2OH CH2OH он он OH OH + H20 OH OH OH но H. но но OH OH OH OH OH OH A. Oxidoreducatase B. Transferase C. Hydrolase D. Lyase NH3 E. Isomerase F. Ligase R-CH-COO "ooc-CH2-CH2-C-COO Amino acid a-Ketoglutarate
Some enzymes can be regulated by covalent modification, in which a group is covalently bonded to an amino acid side chain. Phosphorylation of side chains is a common regulatory covalent modification. In this essay, you will explore phosphorylation of side chains. Compare and contrast the types of interactions a free alcohol side chain such as serine could make with that of a phosphorylated alcohol such as phosphoserine (pSer). Could this modification affect the 3D structure of the protein? How? Imagine you are trying to separate a protein containing an unphosphorylated S residue from the same protein containing a pSer residue. Discuss how you could use ion-exchange chromatography to separate these two proteins
Enolase has a glutamic acid residue in its active site. Describe the experiment that was done that provided evidence for the proposed function of the glutamic acid residue in catalysis by enolase.
CH₂OH 애 H2COPO 2- ATP OH 1 애 애 어 애 The class of the enzyme catalyzing the reaction shown in this figure is a(n) Choose the one best answer. ligase 매 +ADP 매
You are trying to confirm that an enzyme you are studying has the following amino acid in its active site, and that this amino is critical for catalysis: HN- H3NⓇ Which of the following inhibitors could you use to provide evidence of the importance of this amino acid for enzyme function? Tetranitromethane 2,3-Butanedione Diethylpyrocarbonate lodoacetate Nevirapine
Lysozyme catalyzes a "bi-bi" reaction, which means there are (how many) reactants and (how many) products. List, in order, the reactants that bind and the products that are released during a lysozyme-catalyzed reaction cycle -- be succinct but be specific. 1. First reactant = 2. First product = 3. Second reactant = 4. Second product %3D
A reaction in an anabolic pathway is found to have a large negative Gibbs Free energy. How likely is it that this reaction is a regulatory step in the pathway? Explain your answer.

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