3. A biochemistry lab wants to developa method to measure a biochemical transformation in acell by energy consumption that is coupled to the system NAD*/NADH (see below). The HOMO-LUMO gaps (energy needed for the n>n* transition) for the two forms were calculated to be3.12eV and 4.14eV. Based on their structure assign the HOMO-LUMO gaps to either form andassign their UV bands.ADPRibADPRibReductionOxidation0.2NH2ннNH2NAD*NADH250300350400450a (nm)

Here in question, HOMO is Highest Occupied Molecular Orbital and LUMO is Lowest Unoccupied MO…

Answered: 3. A biochemistry lab wants to develop…

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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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
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6. Examine the plot of the enzyme-catalyzed reaction below: Wheat-germ acid phosphatase shows Michaelis-Menten kinetics when acting on para-nitrophenol phosphate 16 14 12 10 8 4 2 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 (S] / mM a) Is this reaction better characterized by Michaelis-Menten kinetics or simple mass action? b) What is the approximate value of Vmax? Km? c) Assuming that this plot was made at 100 nM enzyme, draw the curve, including axis labels, for 300 nM enzyme. d) Imagine that this enzyme is inhibited by a competitive inhibitor with Ki (for inhibitor) = Km (for substrate). Note that v = (kcat [E] tot [S]/Km) / (1 + [S]/Km + [I]/Ki). Draw the curve of reaction velocity (v) versus [S] for [I] = 1 mM. e) Now consider an experiment where you simultaneously introduce substrate and competitive inhibitor at equal concentrations. Make a plot of v versus concentration of [S] = [I], i.e. the X-axis should be the concentration of both I and S, which are equal. v/ uM min-
Table 1. Kinetic parameters of a chosen model wild-type (WT) enzyme and three catalytically-improved mutants (M1 to M3). Enzyme variants k (8¹) WT MI M2 M3 50 500 1000 50 K₁, (μM) 10 100 100 1 k/K (HM¹¹ s¹) 5 The study above was done on a wildtype enzyme and three genetically-engineered mutants. The purpose was to find a mutation to improve the catalytic efficiency of the enzyme for industrial use. Which is the most accurate statement concerning the data? M2 is the optimal choice when substrate concentrations are saturating. The wildtype enzyme is still preferable to M3 when S<
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…
7. Representative values of Vm and ApH for the inner mitochondrial membrane and the thylakoid membrane at 25°C are provided in the table. Vm Арн 1.0 pmf Inner mitochondrial 0.166 V 0.2251 membrane Thylakoid membrane O,1483 0.03 V B) What is the value of AG for the thermodynamically feasible (“downhill") movement of 1 mole of H across the inner mitochondrial membrane?
4. Anammox bacteria are known to obtain energy from the anaerobic autotrophic oxidation of one mole of NH4+ with N02- to form one mole of N2. (1) Develop an electron equivalent energy reaction for the anammox organisms. (2) Calculate ΔGr (kJ/1nol) for this reaction. (3) Calculate fs° for the anammox autotrophic reaction, assuming ε =0.4, N02- is the N source, inorganic carbon is the carbon source and Y is in g VSS/g N.
3. Acetylcholinesterase is a serine hydrolase enzyme im- portant in nerve signal transmission, hydrolyzing acetylcho- line, an ester molecule with a positively charged quaternary nitrogen group. The structure of the physiologically relevant substrate of this enzyme is shown on the right. The quater- H₂C nary nitrogen group serves to anchor the molecule in the active site Gly121 Oxy- anion hole Gly122 Ala204 Substrate ACh His447 Catalytic triad Ser203 Glu202 Glu334 Ser229 CH3 N+ CH3 CH3 The a Scale document down rine protease family, consisting of a catalytic triad Ser203- His447-Glu334 with Ser203 supplying the nucleophilic hydroxyl group and an oxyanion hole com- prised of peptide NH groups of Gly121, Gly122, and Ala204, illustrated in the diagram above, for which carbon (green), nitrogen (blue), and oxygen (red) atoms are shown while hydrogen atoms are white. The enzyme catalyzed reaction can be represented by the following scheme: (a)( k1 K2 E + S = ES K-1 K3 EYE + P where ES…
2. a. Label the following structures as ATP, ADP, AMP, P₁, PPi, or Adenosine. Place your answers in the boxes provided. HO H OH H OH OH O N. H H OH + ATP NH₂ . + ADP 01210 ++++++ O-AMP O O Adenosine *+-+ O 0=210 HO b. Put an "X" in the box for the reaction that is thermodynamically most favorable. OH OPP OPP Adenine + AMP + Adenosine
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?
4
11. Refer to the figure below. нн Н `NH2 NH2 N' N- 2e-+H* R NAD+ NADH NAD+ functions as a coenzyme in many enzyme-catalyzed reactions. The changes that take place in this coenzyme are the same for all of these reactions and are illustrated in the figure. It is likely that, in these reactions, NAD+ functions as an electron acceptor (reducing agent) in redox reactions. functions as an electron donor (oxidizing agent) in redox reactions. functions as a base in acid-base catalytic mechanisms. functions as an electron donor (oxidizing agent) in redox reactions. functions as an electron acceptor (oxidizing agent) in redox reactions. +Z-

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