о6. What is the catalytic triad and what particular protein family would you find this? Whatis the general role of the catalytic triad? Predict what would happen if Asp weremutated to Gly.ructure formation of alpha heli

Serine proteases are protein cleaving enzymes that have Serine, Histidine and Aspartate (the…

Answered: 6. What is the catalytic triad and what…

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. Draw the ringed form of D-glucose with the following modifications: (a) Convert to sugar acid at C-6. Name this one! (b) What if that molecule is modified to ALSO have a -COOH at carbon 1? Draw its Fisher projection and what it is named? (c) How might the COOH group(s) lead to new chemical functionality?
8. In a separate enzyme happyase experiment using [Et] = 10 nM, the reaction velocity is measured at 3 uM s-l. What is the [S] used in this experiment? Kcat = 600s-
3. (a) In Bakers yeast there are two variants of cytochrome c, a heme containing protein of 108 amino acid residues that catalyzes electron transfer reactions in mitochondria. The two forms of cyto- chrome c known as iso-1 and iso-2 cytochrome c differ in 17 of the 108 amino acids. The content of proton dissociable side chains for the two cytochromes c is given in the table below: Side chain pka iso-1 cytochrome c Ziso-1 iso-2 cytochrome c 12.5 3 4.0 4 8.0 4.0 6.0 10.0 9.0 7.0 4.0 Arginine Aspartate Cysteine Glutamate Histidine Lysine Tyrosine -NH3Ⓡ -COOH 1 4 4 16 5 1 1 What is the overall electrostatic charge on each cytochrome at pH 8? (b) To the right is a diagram of the chemical groups in carboxymethyl-cellulose and DEAE-cellulose that are used for ion exchange chromatography to purify proteins. At pH 8 which chromatographic resin has to be used to separate iso-1-cytochrome c from iso-2-cytochrome c from a lysate of yeast cells? If the proteins are separated by application of a…
2. The diagram to the right shows the change in the structure of the C-terminal portion of each of the ẞ-subu- nits of human hemoglobin (HbA) in the oxyHb to deox- yHb or R-to-T transition. The hydrogen bonding interac- tion of the C-terminal ẞHis 146 residue with the side chain of Asp94, highlighted by the red ellipse, has been shown to be responsible for a major portion of the proton uptake associated with the Bohr effect. Treatment of HbA with the enzyme carboxypeptidase A (CPA) results in loss of the C-terminal ẞHis 146 and ẞTyr145 residues of the ẞ- subunits. (a) ( ) Draw a Hill plot [log(Y/[1-Y]) vs. log(pO2), Y = fraction of heme groups occupied by O2] to compare the values of the Hill coefficient nн and the O2-binding affinity at pH 7.4 of normal HbA before and after treat- ment of with CPA. (b) (' ) How will the plot for CPA-digested HbA change at pH 7.2? (c) 1 Hi5146 HN- ✓ Low PK B-chain. CH2 CH-NH-CO-CH-NH- CH₂ Tyr145 он HbO2 or R state Туг145 CH-CH2- OH co NH CH CH₂ His…
2. Chymotrypsin, trypsin, and elastase are members of a family of enzymes referred to as serine proteases. The enzyme papain (found in papaya) is also a protease but is a member of a family of enzymes referred to as cysteine proteases. The amino acid residues in the active site of papain critical for peptide bond hydrolysis are a protonated histidine and a deprotonated cysteine residue. The cysteine residue functions as the nucleophile similarly to the serine residue in serine proteases. (a) Using what you know about chymotrypsin's mechanism, draw a reaction mecha- nisn for the hydrolysis of a peptide bond by papain. Does the mechanism you have drawn employ acid-base catalysis, covalent catalysis, (b) or both? (c) The pKa values of the active site residues that control the pH profile of the activity of pa- pain are 4.2 and 8.2. The pH optimum for the reaction is 6.0. Through the many years of re- search carried out on cysteine proteases, it has been demonstrated that the pKa of 4.2…
2. Phospholipases (PL) are enzymes that hydrolyzes PLA1 phospholipids into fatty acids and other lipophilic substances. Different class of phospholipase cleaves different bond in a phospholipid molecule. Shown on the right are the cleavage sites of four classes of PL: PLA1, PLA2, PLC, and PLD. R1 R2 -O-P-'·O-R3 (a) Write down the reaction of phosphatidylcholine (PC) cleaved by PLA2. Suppose the two acyl groups are R1 and R2 as shown in the figure. Make sure the chiral carbons in the reactions have the right stereochemistry (i.e., use wedge-dash notation), and the charges on the atoms reflect the molecule in neutral pH. PLA2 PLC PLD (b) Which PL is needed in order to release choline for salvage? (c) What is the structure and name of the remaining molecule after cleaving PC by the PL in (b) and releasing choline. No need to use wedge-dash notation. (d) The molecule in (c) can be used to synthesize triacylglycerol. Write down the reactions, including the enzymes and cofactors. Assume the…
4
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…
9. Shown below is a binding pocket for a protein with a ligand bound. The ligand interacts with a serine and a valine side chain. ligand a. Briefly explain, in terms of Ka, the effect of a mutation that replaces the serine residue with a valine residue. b. Briefly explain, in terms of Kd, the effect of a mutation that alters the ligand (as seen below) binding to the original, unmutated, binding site. :0: ligand 2
The catalytic triad consists of Asp, His, and Ser. What would be an alternative for histidine and how would we draw the interactions in a mechanism?
10. How many reducing ends are in a molecule of potato amylopectin that contains 500,000 residues with a branch every 250 residues? Explain your answer.
3. Aspartate aminotransferase (AspAT) catalyzes the following reaction: COO™ C=O CH₂ COO Oxaloacetate The AspAT enzyme has two active-site arginines, Arg 386 and Arg 292, that interact with the a- carboxylate and ß-carboxylate groups on the aspartate substrate, respectively. Investigators stud- ied the mechanism of AspAT in more detail by constructing mutant AspAT enzymes in which either or both of the essential arginines were replaced with a lysine residue. The kinetic parame- ters for the wild-type enzyme and nutant enzymes are shown in the table. NH—CH-COO T CH₂ COO™ Aspartate α-Amino acid Enzyme 1. Wild-type Asp AT(Arg 292 Arg 386) 2. Mutant Asp AT(Lys 292 Arg 386) 3. Mutant Asp AT(Arg 292 Lys 386) 4. Mutant Asp AT(Lys 292 Lys 386) Asp-AT a-Keto acid KM (MM) 4 326 72 300 Kcat (S-1) 530 4.5 9.6 0.055 (a) The Michaelis constant is strictly not equivalent to an equilibrium binding constant; however under certain conditions the Michaelis constant does approach the equilibrium (dissoci-…

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6. What is the catalytic triad and what particular protein family would you find this? What is the general role of the catalytic triad? Predict what would happen if Asp were mutated to Gly.