1. You are working on an experiment with a newly discovered enzyme. This enzyme works mostefficiently at a pH of 7.70. You make 250 mL of a 150 mM phosphate buffer, pH 7.70. (pK = 6.82).a. What are the concentrations of the weak acid and conjugate base forms of this phosphatebuffer when you start the experiment?b. In the process of the enzyme catalyzed reaction, 25 mM acid (H+) is produced. What is thepH of the solution after the reaction is complete? Assume no change in volume byproduction of the acid.2.Case Study Questions:Normal Levels of Substances in the Arterial Blood:PH7.40 + 0.05pCO2 (partial pressure of carbon dioxide)40 mm HgpO2 (partial pressure of oxygen)Hemoglobin - O₂ saturation[HCO3-]90-100 mm Hg94 - 100%24 meq / literA. Kim is a 38 year old woman admitted to the hospital for bulimia. Her laboratory results are asfollows: pH 7.48, pCO₂ in the normal range and total HCO3 higher than normal. Classify her acid-base balance as acidosis or alkalosis and as metabolic or respiratory and fully explain yourreasoning for your choicePropose the mechanism by which bulimia contributed to the lab results seen here Include theequilibrium expressions chemically leading to this condition

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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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1. Enzyme X has a molecular weight of 35,000 Da. When this enzyme is assayed for enzyme activity, the corresponding line of the double reciprocal plot has the equation y = 75,253X + 102,392. The substrate concentration was in mM and the velocity was measured in mM min". From these data calculate the following: a. KM and Vmax b. kcat if the enzyme concentration was 2 mg/mL. 2. When you run enzyme X from question one on an SDS-PAGE you find that, after Coomassie staining, there is only one band on the gel that runs just below the 20,000 Dalton molecular weight marker. What does this result tell you about the nature of the quaternary structure of your enzyme?
What would be the best buffering agent to choose if you wanted to buffer an enzyme reaction or tissue culture medium at pH = 7.95? Group of answer choices a. HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid); pK = 7.5 b. Histidine; pK1= 1.78; pK2= 5.97; pK3= 8.97 c. Bicarbonate; pK = 6.1 d. Phosphate; pK1 =2.0, pK2 = 6.8; pK3 = 12.5 e. Tris or Tris(hydroxymethyl)aminomethane; pK = 8.07
You have performed protein purification on your new favorite enzyme using a protocol which involves the following steps/samples: crude extract, ammonium sulfate cut, ion exchange and gel filtration. You need to run 25ug of protein from your crude extract sample on an SDS-PAGE gel. You have determined that the protein concentration of your crude extract sample is 2.1mg/ml. Your total sample volume is 30ul. You have water for your diluent and 6x SDS-loading dye to prepare your sample. List the components of your prepared sample. Note: you will only have access to a P20 and a P200 to prepare this sample.
1. A Lineweaver-Burk Plot is shown below. 30 25 Curve A y = 3.1207x + 2.4978 20 15 Curve B y = 1.0003x + 2.3602 10 5 -3 1 5 7 11 1/[Catechol] (mM1) With these curves, determine the following enzyme parameters. Show all pertinent solutions. a. Km of Curve A and Curve B b. Vmax of Curve A and Curve B c. Assuming that one of these curves corresponds to the kinetics of one enzyme and one substrate, which curve represents the effect of an inhibitor? Why do you say so? d. What type of inhibition is exhibited by your answer in question c? Why do you say so? 1/V, (units of activity 1)
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…
4) Enzyme 1 and 2 catalyze the same reaction. Both enzymes have the same Km, but Enzyme 1 has a higher Vmax. A. Sketch out what both enzymes look like in a lineweaver burk plot. B. You test an inhibitor (compound A) on both enzymes. In Enzyme 1 The apparent Km increases, in enzyme 2 both the Km and Vmax decrease. What does this suggest about what kind of inhibitor compound A is in each enzyme?
You run a series of assays at 25°C on enzyme A. You measure the velocity for a range of S concentrations. What is the Km (in mM) for Enzyme A?
A purified protein sample was used in a reaction, resulting in an activity of 696.7 nmol min-1. The reaction volume was 145.0 µL and the final volume before loading the plate was 1,050 µL. The total reaction time was 4.25 min. The amount of protein used in the reaction was 4.270 µg. Calculate the specific activity of the sample (in nmol min-1 µg-1).
Sucrase has an optimum temperature of 37°C and an optimum pH of 6.2. Determine the effect of the following on its rate of reaction: 1) no change 2) increase decrease 3) A. increasing the concentration of sucrase B. changing the pH to 4.0 C. running the reaction at 70°C What are the functions of Allosteric enzymes What are some factors that affects enzyme activity? I. II. III. IV. V. VI. Enzyme activity can be regulated by allosteric enzymes, feedback control, and covalent modifications. T/F Examples of Zymogens are the proteases trypsinogen and chymotrypsinogen. T/F? Trypsin catalyzes the removal of dipeptides from inactive chymotrypsinogen and trypsinogen to give the active proteases chymotrypsin and trypsin. T/F The removal of a polypeptide chain from proinsulin produces the active form of insulin. T/F? A kinase can activate an inactive enzyme by phosphorylation, ie adding a phosphate group. T/F? A phosphatase can activate an inactive enzyme by removal of phosphate. T/F? Identify…
1. Penicillin is hydrolyzed and thereby rendered inactive penicillinase, an enzyme present in some penicillin-resistant bacteria. The molecular weight of this enzyme in Staphylococcus aureus is 29.6 kilo Daltons (29.6 kg/mole or 29,600 g/mole or 29,600 ng/nmole) The amount of penicillin hydrolyzed in 2 minute in a 10-mL solution containing 109 g (1 ng) of purified penicillinase was measured as a function of the concentration of penicillin. Assume that the concentration of penicillin does not change appreciably during the assay. [Hint: Convert everything to the same concentration terms] Show all calculations and include spreadsheets and graphs to determine Km, Vmax and kcat for this enzyme. Make sure your final answers have correct units. [Another hint: Note that [S] and amount hydrolyzed are already in concentration terms. So you don't need to worry about the volume for calculating [S] and V. ] Penicillin concentration (microM) Amount hydrolyzed (nanoM) 1 110 3 250 5 340 10 450 30 580…
3.An enzyme catalyzed reaction is studied and the following kinetic analysis is obtained: |[S), mM 0.050 0.075 v, (µM min") 0.93 1.264 1.77 2.14 3.7 0.125 0.175 0.935 a. Using Excel, make a fully labeled Lineweaver-Burk plot and determine the Km and Vmax for the enzyme b. The reactions were set up dissolving 1 mg of the enzyme (MW= 100000 Da) in 100 ml of final reaction buffer. Determine the turnover number for the enzyme assuming 1 active site exists per enzyme molecule? c. Determine the catalytic efficiency for the enzyme d. The same reactions are performed in presence of an inhibitor A and the resulting velocities determined: v plus inhibitor, (µM min) 0.272 0.37 0.518 0.626 |1.08 |[S), mM 0.050 0.075 0.125 0.175 0.935 Plot these data on the same graph as above and determine the new Km and Vmax and the type of inhibitor (competitive, non-competitive). e. Can the effects of the inhibitor be over-ridden by adding more substrate? Why?
1. Calculate the pH of a 0.05 M solution of HCl. 2. Calculate the pH of a 0.1 M solution of NaOH. 3. Calculate the pH of an acetic acid solution in which [CH3COO - ] = 0.037 M and [CH3COOH] = 0.044 M. (pKa = 4.76) 4. You are conducting a biochemical experiment with an enzyme that has optimal activity at pH = 10.00. You decide to use carbonate (pKa1 = 6.38, pKa2 = 10.30) as the buffer to keep the pH stable throughout the enzymatic reaction. (Recall that the formula for carbonic acid is H2CO3.) You prepare a 0.5 M solution of carbonate buffer at pH = 10.00. Calculate the concentrations of the major carbonate species in your solution. 5. Calculate the pH of the buffer solution in which [H3PO4] = 0.038 M and [H2PO4 - ] = 0.046 M (pKa1 = 2.12, pKa2 = 7.21, pKa3 = 12.32). 6. Add 5.0 mL of 0.1 M NaOH to 80 mL of buffer from question 5 and calculate the pH.

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