Exam 3 – Fall 2019 BCH 341 - Physical Chemistry with a Biological Focus Professor Jeff Yarger September 4-7, 2019 DUE Monday October 7, 2019 by 11:59 PM (UTC-7). Turn in completed exam as a typeset single PDF document into the assignment link on ASU Canvas. Please make sure the completed exam is organized, self-contained and all text, equations, numbers, units, figures and images are typeset, clear and legible. Student Required Identification: NAME:___rubric/key________________________________________ ASU ID #:________________________________________________ (10-digit number (typically starting with 12xxxxxxxx or 10xxxxxxxx)) Email: [email protected]_________________________ Exam General Instructions There are 4 multi-component exercises/projects on this exam. Each of the multi-component numbered exercises/projects (problems) is worth 25 points. Hence, the exam is worth a total of 100 points. You are required to explicitly show all equations, numerical calculations and associated units. All points are associated with explicitly showing all your work and no points are awarded for just determining the correct numerical answer. All assumptions need to be clearly and concisely stated. If thermodynamic parameters are used, the citation, reference or link to where this thermodynamics data came from must be stated. Appropriate units should be associated with all numerical problem solving. The completed exam should be typeset (no handwriting of equations or numerical values and associated units). Evaluation Section (TA/Instructors) Instructor Comment: ___________________________________________________________________________________________ ___________________________________________________________________________________________ ___________________________________________________________________________________________ ___________________________________________________________________________________________ Instructor Grading Summary: Exam Score: ________ / 100 pts Extra Credit: ________ / 15 pts
Transcript
Exam 3 – Fall 2019
BCH 341 - Physical Chemistry with a Biological Focus
Professor Jeff Yarger
September 4-7, 2019
DUE Monday October 7, 2019 by 11:59 PM (UTC-7). Turn in completed exam as a typeset single PDF
document into the assignment link on ASU Canvas. Please make sure the completed exam is organized,
self-contained and all text, equations, numbers, units, figures and images are typeset, clear and legible.
Student Required Identification:
NAME:___rubric/key________________________________________ ASU ID #:________________________________________________ (10-digit number (typically starting with 12xxxxxxxx or 10xxxxxxxx)) Email: [email protected]_________________________
Exam General Instructions There are 4 multi-component exercises/projects on this exam. Each of the multi-component numbered
exercises/projects (problems) is worth 25 points. Hence, the exam is worth a total of 100 points. You are required
to explicitly show all equations, numerical calculations and associated units. All points are associated with
explicitly showing all your work and no points are awarded for just determining the correct numerical answer.
All assumptions need to be clearly and concisely stated. If thermodynamic parameters are used, the citation,
reference or link to where this thermodynamics data came from must be stated. Appropriate units should be
associated with all numerical problem solving. The completed exam should be typeset (no handwriting of
equations or numerical values and associated units).
1. Malate dehydrogenase (MDH) is an enzyme that reversibly catalyzes the oxidation of malate to oxaloacetate
using the reduction of NAD+ to NADH. This reaction is part of many metabolic pathways, including the citric
acid cycle. (A) Write a balanced chemical reaction and the associated half-reactions for the oxidation of malate to
oxaloacetate using the reduction of NAD+ to NADH. (10 pts) (B) Calculate the biological standard Gibbs energy
for the balance chemical reaction of the oxidation of malate to oxaloacetate using the reduction of NAD+ to
NADH. (15 pts)
This exam question was directly adopted from the Fall 2019 BCH341 suggested homework problem 5.35(b) -
Atkins and De Paula, Physical Chemistry for the Life Sciences, 2nd Ed. p. 214.
Also, there is a YouTube video created as part of an Honors Contract that covers 5.35(b) and is posted (with the
student's permission) on the biopchem channel:
https://youtu.be/cfnInDizyvY
The solution given by Trapp and Cady, Solution Manual to Accompany Physical Chemistry for the Life Sciences,
2nd Ed., for 5.35(b) is provided below:
Other than showing explicitly showing both 1/2 reactions, this basically covers the solution for problem 1.
There are a lot of sources that can be used to get the biological standard potentials, including Table 5.2 in Atkins
textbook. This is what was used to determine the reaction standard potential used in the solution manual (but not
explicitly calculated). As long as the source for the biological standard potentials used by students is given and
can be verified, it should be allowed. From values I have found in other textbooks and online, the values can vary
by ~10%.
Page 3
2. The standard potentials of proteins can be determined using a solution method by allowing the oxidized protein
to react with an appropriate electron donor and then using the Nernst equation, the equilibrium concentrations of
all species in solution, and the known standard potential of the electron donor. We shall illustrate this method
with the protein cytochrome c.
(A) The one-electron reaction between cytochrome c, cyt-c and 2,6-dichloroindophenol, D, can be written as
cyt-cox + Dred ⇌ cyt-cred + Dox
Consider Eocyt and EoD to be the standard potentials of cytochrome c and D, respectively. Show that, at
equilibrium (eq), a plot of ln([Dox]eq/[Dred]eq) against ln([cyt-cox]eq/[cyt-cred]eq) is linear with a slope of 1 and y-
intercept F(Eocyt-EoD)/RT, where equilibrium activities are replaced by the numerical values of equilibrium molar
concentrations. (10 pts)
(B) The following data were obtained for the reaction between oxidized cytochrome c and reduced D at pH 6.7
buffer and 298 K. The ratios [Dox]eq/[Dred]eq and [cyt-cox]eq/[cyt-cred]eq were adjusted by adding known volumes of
a solution of sodium ascorbate, a reducing agent, to a solution containing oxidized cytochrome c and reduced D. From the data and the standard potential of D of +0.237 V, determine the standard potential of cytochrome c at
pH=6.7 and 298 K. Show and describe all plots and fits of the data for full credit. (15 pts)
