## Educational Resource: Understanding Biochemical Reactions### 5. Reaction for Assembly of a Tetrapeptide**Equation:**- Serine + Proline + Alanine + Methionine → SPAM tetrapeptide**Questions:**- 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. - [Space for Student's Answer]### 6. Reaction Involving Glutamate Synthesis**Equation:**- Glutamic acid + Ammonia + ATP → Glutamate + ADP + Pi**Questions:**- Is this reaction **anabolic** or **catabolic**?- Is this a **positive** or **negative** delta G reaction? **Explanation:**- This is actually an example of a **coupled reaction**! Briefly, explain why reaction coupling is required, and how it works in this example. - [Space for Student's Explanation]### Graphs and DiagramsThis section includes no diagrams or graphs to explain. If there were, a detailed description would be provided here.---This resource helps in analyzing biochemical reactions, focusing on whether they are building up (anabolic) or breaking down (catabolic) and understanding the energy changes that occur during these processes (delta G). Coupled reactions are also highlighted, emphasizing their role in cellular processes.

Cellular metabolism consists of both anabolic and catabolic processes. The energy released during…

Answered: 5. Consider the reaction for assembly…

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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5. Suppose an enzyme needed a cysteine thiol (sulfhydryl) group for its catalytic activity, and catalysis required the Cys thiol to act as a nucleophile at the beginning of the catalytic cycle. That would mean the Cys residue had to be in its UNPROTONATED (conjugate base) form. If that particular Cys residue in that protein had a pKą of 7.5, what fraction (percent, or proportion) of the total enzyme molecules would have the Cys R group in its ACTIVE form at pH 7.0?
1. You need 0.5 liter of a 0.1 M buffer for a biochemical reaction that you plan to perform at pH 2.0. On the shelf in your laboratory you have available phosphoric acid, and the amino acids aspartate, glycine, glutamate, tyrosine, and histidine (all you have available are the fully deprotonated forms of the molecules); these are the only buffer materials you have available. (The pKa values for these compounds are given below.) For phosphoric acid, pKal1 = 2.12, pKa2 = 7.21, and pKa3 = 12.32 For aspartate, pKaCOOH = 1.88, pKaNH3+ = 9.60, pKa sidechain = 3.65 For glycine, pKaCOOH = 2.34, pKaNH3+ = 9.60 For glutamate, pKaCOOH = 2.19, pKaNH3+ = 9.67, pKa sidechain = 4.25 For histidine, pKɑCOOH = 1.82, pKɑNH3+ = 9.17, pKa sidechain = 6.00 For tyrosine, pKaCOOH = 2.20, pKaNH3+ = 9.11, pKa sidechain = 10.07 a. Of these possible buffers, which is likely to yield the greatest resistance to pH change from the starting pH of 2.0, assuming that you were going to run a biochemical reaction that…
10. Procaine is known to undergo faster metabolic hydrolysis than procainamide. Give explanation. -NET2 -NEt2 HN H2N- H2N- Procainamide Procaine 11. In phase 2 metabolic transformation chloramphenicol the primary alcohol is converted to a glucuronide conjugate. Draw chemical structure of the product. Provide the name of enzyme that catalyze this metabolic reaction. он ? CHCI2 O2N- но
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5. Given the following information tables, determine in which cell type cleavage of the terminal phosphate from ADP yields the greatest actual change in free energy. (Please work in kJ/mol.) TABLE 13-6 Standard Free Energies of Hydrolysis of Some Phosphorylated Compounds and Acetyl-CoA (a Thioester) TABLE 13-5 Total Concentrations of Adenine Nucleotides, Inorganic Phosphate, and Phosphocreatine in Some Cells AG (kJimol) (kcalimol) Concentration (MM) Phosphoenolpyruvate 1,3-Bisphosphoglycerate (+3-phosphoglycerate + P) Phosphocreatine -61.9 -14.8 ATP ADP AMP P, PCr Rat hepatocyte Rat myocyte 49.3 -11.8 3.38 1.32 0.29 4.8 -43.0 -103 8.05 0.93 0.04 8.05 28 ADP (+ AMP + P) -32.8 -7.8 -7.3 Rat neuron 2.59 0.73 0.06 2.72 4.7 ATP (+ ADP + P) Location of -30.5 Human erythrocyte 225 0.25 0.02 1.65 ATP (+ AMP • PP) AMP (+ adenosine P) cleavage is important! 45.6 -10.9 E. coli cell 7.90 1.04 0.82 7.9 -14.2 -34 For erythrocytes the concentrations are those of the cytosol (human erythrocytes lack a…
1. Depict the structure features in the active site of cysteine protease 2. provide a step-wise reaction mechanism to show the hydrolysis of the peptide bond catalyzed by a cysteine protease
a. Suppose that you have the peptide Ala-Gly-Tyr-His-Leu and you treat it with FDNB and then 6M HCl. Draw the structures of all the products that you will have in solution (assume all reactions to go to completion).
7. Chalcone isomerase catalyzes the reaction illustrated below. A series of modification experiments were performed on this enzyme to identify which amino acid residues might be in the active site and which might promote the cyclization reaction. OH Ho. Но Explain the following results: A) Acetic anhydride treatment inhibited enzyme activity. B) Pyrocarbonate inhibited activity and was found to modify 7 residues. However, this enzyme only contains 6 His and modification of these did not affect activity. C) lodoacetate inhibited activity but this effect coult be decreased in the presence of substrate or product. D) Methane methanethiol sulfonate modified the enzyme but did not inhibit catalytic turnover. In addition, this modification was reversed in the presence of B-mercaptoethanol. keNyons Rengent
Cysteine proteases are enzymes that degrade proteins. You may have heard of some examples of these types of proteins before! Bromelain is an enzyme found in pineapple that is commonly used as a meat tenderizer and is the reason Jell-O with fresh pineapple will not solidify. Cysteine proteases are remarkably similar to serine proteases (like chymotrypsin), except they have a cysteine in their active site rather than a serine. Using the mechanism that we discussed for serine proteases, draw a corresponding mechanism for a cysteine protease cleaving the bond between an alanine-glycine dipeptide. Note that cysteine proteases do not require an aspartate in their active site. Also note that the cysteine is usually in its thiolate form (deprotonated) and the histidine is in its imidazolium form (fully protonated) in the resting state of the enzyme.
9. Bacteria can synthesize tryptophan, tyrosine, and phenylalanine through a series of biochemical reactions. All three amino acids are derived from the same precursor molecule, as shown in the diagram below. OH но OH Common Precursor Anthranilate Chorismate Synthase Mutase OH NH2 00 Trp Precursor Tyr/Phe Precursor a. A majority of this precursor is used by the enzyme chorismate mutase to synthesize another precursor that is used to make phenylalanine or tyrosine. Experimental data shows that when there is a high concentration of phenylalanine in a cell, more tryptophan is produced. This data also suggests that phenylalanine binds to chorismate mutase but does not bind to the enzyme's active site. Use what we learned in class to describe how this binding could regulate chorismate mutase's activity and result in more tryptophan being produced. b. The common precursor is also a substrate for a second enzyme, anthranilate synthase. The product of that reaction is a precursor for…
3. One strategy for designing an antiviral drug against hepatitis C virus (HCV) is targeting on the viral protein NS3-4A protease, an enzyme breaking the peptide chain through a nucleophilic acyl substitution reaction on amide. The designed drug Narlaprevir with a keto amide functional group acts as a protease inhibitor undergoing a nucleophilic addition reaction. 1) Propose a reasonable mechanism for protease (viral enzyme) breaking the viral protein Enz-OH (Viral protease) R Enz НА H2N R Viral protein O:
7. During amino acid catabolism, how is amino group removed and excreted in the form of urea? Please write the reactions starting from a generic amino acid to the formation of urea. Please indicate the names of enzymes, cofactors, names of substrates, and products of each reaction and the location of the reaction i.e. whether in cytoplasm or mitochondria.

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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.