Final Exam – Spring 2019

BCH 341 - Physical Chemistry with a Biological Focus

Prof. Jeff Yarger and Prof. Vladimiro Mujica

Feb 23-25, 2019

DUE Monday, Feb 25, 2019 by 11:59 PM (UTC-7). Turn in completed exam as a single PDF document into the

assignment link on ASU Blackboard. Please make sure the completed exam is organized, self-contained and legible.

Name: ______________________________________________ (as recorded on ASU Blackboard)

ASU Email: _______________________________ ASU ID: ____________________________

There are 12 physical biochemistry problems on the final exam, the first 10 are regular questions and the

last two, which require some additional effort are extra credits. The problems are designed to evaluate

student’s knowledge and ability to solve biochemical problems in the primary areas of thermodynamics

and kinetics. Each exam problem is worth 30 points for a total of 300 points, the extra credit questions are

also worth 30 points each. The majority of the points for each problem are given for the setup and

systematic step by step method (logic) used to solve each problem. Most final solutions are numerical.

However, the numerical answer alone is not sufficient to receive credit for solving the problem. A detailed

methodology is required. An example of a common problem solving methodology is (i) restate the

problem or question; (ii) define or sketch the system; (iii) express the relevant principles, laws, postulates,

axioms in a form suitable to the system and/or process; (iv) determine what properties are involved and

how to find values for them (write down the principle equations or tables); (v) describe the process in

terms of the changes in system properties (typically involves sorting the information into initial property

values, final property values and transfer properties); (vi) substitute the known property values and process

relations into the principle equations; (vii) calculate the desired quantities (answers) and check their

reasonableness (and associated units). This represents one general method used for general problem

solving in the biological, chemical and physical sciences. However, it is by no means unique or universal.

Problem solving in the area of biochemistry and physical chemistry can take on many paths and methods.

The evaluation does not depend on the exact path or method, just on its logical consistency and its ability

to follow step-by-step the path, equations, mathematics and calculations used to solve each problem. The

final numeric answer is roughly worth 10%, the other 90% of the points come from evaluating a student’s

methodology and ability to show a consistent logical path (typically mathematically) to solving each

problem.

This is a long-winded way of telling students to show all work in solving each problem. Also, be

organized and legible when you show your step-by-step work for solving each problem.

Total Points (300 possible): _________

1. Consider two large bodies with identical heat capacities. The two bodies are

initially at different temperatures, Th and Tc, respectively, with Th > Tc. They are

then allowed to come into thermal contact and heat is transferred from one body

to the other. The total entropy change for this thermodynamic process is

Δ𝑆𝑢𝑛𝑖𝑣 = Δ𝑆ℎ + Δ𝑆𝑐 =𝑞ℎ

𝑇ℎ+

𝑞𝑐

𝑇𝑐

The first law of thermodynamics requires

Δ𝐸𝑢𝑛𝑖𝑣 = Δ𝐸ℎ + Δ𝐸𝑐 = 𝑞ℎ + 𝑞𝑐 = 0.

Which means that 𝑞ℎ = −𝑞𝑐, but no indication is given about the spontaneous

direction of heat transfer. However, the total entropy must increase and this

determines the sign and direction of the heat transfer. Which of the following

statements is correct?

a. 𝑞ℎ < 0, 𝑞𝑐 > 0 b. 𝑞ℎ > 0, 𝑞𝑐 < 0 c. There is not enough information to establish the sign and direction of

heat flow.

2. The accompanying diagram shows how the free energy, G, changes during a

hypothetical reaction A(g)+B(g)=C(g), at constant temperature and pressure as a

function of the progress of reaction. On the left are pure reactants A and B, and on

the right is the pure product, C. Is the following statement true or false? Justify

your answer.

The minimum in free energy at the equilibrium state corresponds to a maximum

in entropy of the system and its surroundings.

G

Progress of Reaction

x

3. Consider the following sequential reaction scheme:

(A) Plot (Graph) the concentration profiles ([A], [I] and [P] versus time) for the above

sequential reaction where the rate constant for A→I is 0.5 inverse seconds and one-half the

rate of I→P (i.e., kA = ½ kI = 0.5 s-1).

(‘Plot’ does NOT mean ‘sketch’ the concentration profile. Plot is referring to graphing or

specifically in this case using a mathematical diagram using Cartesian coordinates to display

values for two variables for a set of data)

(B) Determine the time at which [I] is at a maximum for the above sequential reaction, i.e.,

kA = ½ kI = 0.5 s-1. [Express your answer in units of seconds. Put a box around your answer]

4. Arrhenius equation is an empirical law for the rate constant of a chemical reaction

𝑘 = 𝐴𝑒−𝐸𝐴/𝑅𝑇

where A is called the pre-exponential parameter A and is the activation energy of the

reaction.

Arrhenius parameters A and EA for three different chemical reactions are given in

the table below

Reaction A EA

cyclopropene → propane (1st order) 1.58 x 1015 s-1 272 kJ mol-1

cyclobutane → 2C2 H 4 (1st order) 3.98 x 1015 s-1 261 kJ mol-1

CH 3 (g) + CH 3 (g) → C2 H 6 (g) (2nd order) 2.00 x 1010 dm3 mol-1 s-1 0 kJ mol-1

(i) Draw a schematic plot of ln k against 1/T for the three reactions.

(ii) Which reaction is more sensitive to temperature?

5. The concentrations of the principal ions in a sample of intracellular fluid are 20.0 mM for

sodium chloride, 15.0 mM for potassium chloride, 5.0 mM for sodium hydrogen

phosphate, 2.0 mM for magnesium phosphate tribasic, and 2.0 mM for potassium

nitrate. Calculate the ionic strength of the intracellular fluid.

[Put a box around your final answers. Express your answer in units of mM.]

6. What is the concentration of hydrofluoric acid (Ka=6.8 x 10-4) in a solution with a

pH of 3.65 ?

7. When you put water in your freezer to make ice, it is common for this water to

‘supercool’ before freezing into ice. A ‘supercooled liquid’ is defined as a liquid that has

a temperature below its freezing point. Let’s look more closely at the thermodynamics of

this common process that happens in your freezer. Calculate the change in enthalpy (ΔH)

and entropy (ΔS) as accurately as possible for the process of taking 10.0 ml supercooled

liquid water (H2O (l)) at a temperature of -15oC and having it solidify into ice (H2O (s))

with a final temperature of -15oC. [Put a box around your final answers for ΔH and ΔS]

8. Radicals, very reactive species containing one or more unpaired electrons, are

among the by-products of metabolism. Evidence is accumulating that radicals are

involved in the mechanism of aging and in the development of a number of

conditions, ranging from cardiovascular disease to cancer. Antioxidants are

substances that reduce radicals readily.

a. Which of the following known antioxidants is the most efficient (from a

thermodynamic point of view): ascorbic acid (vitamin C), reduced

glutathione, reduced lipoic acid, or reduced coenzyme Q?

b. What type of additional information about the chemical reactions involved

in the action of an antioxidant would be required to answer the same

question but this time in terms of the kinetic efficiency?

9. The following plot is a sketch of a reaction profile for a reaction with three steps

labeled A, B, and C on the plot.

a. RDS in the plot corresponds to the rate determining step for this reaction.

Why?

b. How many intermediate states can be identified in this reaction profile?

c. How many activated states can be identified in this reaction profile?

d. Based on this reaction profile, suggest a plausible mechanism for this

reaction. Identify equilibrium and irreversible steps, intermediates, and

label appropriately the rate constants.

10 Find one or two articles in the literature that discuss the concept and implications

of catalysis in confined spaces as a model for enzymatic activity in cells. An

example of such a literature is available in the following link

https://onlinelibrary.wiley.com/doi/pdf/10.1002/cphc.201800058

Summarize your reading and the discussion in these papers. Use the concepts

about catalysis that you have learned in BCH 341.

11. The action of enzymes is often described as following a two-step mechanism,

named after the biochemists Michaelis and Menten, where in the first step the

enzyme and the substrate form an intermediate complex, and in the second

step the enzyme is released and the product is formed. Schematically,

E + S ⇆ ES (fast) , k1 and k-1 are the rate constants for the direct and reverse

reactions respectively.

ES → E + P (slow), k2 is the rate constant for the reaction.

where E=enzyme; S=substrate; ES=enzyme-substrate intermediate complex, and

P=product.

If an enzymatic reaction follows this mechanism, what rate law is expected for the

reaction?

12. Over the last few years, hemp seems to be a growing social and medical topic. The

primary active pharmaceutical ingredients (API) in hemp plant and associated extracts is

the general class of chemical compounds called cannabinoids. The most notable

cannabinoid in hemp is cannabidiol (CBD). The majority of cannabinoids produced from

the hemp plant are found in a carboxylic acid form. This includes CBD, which is actually

found as cannabidiolic acid (CBDA) in living hemp plants. The process of going from

CBDA to CBD is decarboxylation. To date, the thermodynamics and kinetics of

decarboxylation in CBD has not been studied rigorously. However, the great thing about

thermodynamics of such a common reaction, like decarboxylation, is that it is still

possible to estimate the expected thermodynamics energies based on (i) computational

analysis, (ii) arithmetic methods or based on (iii) comparison to decarboxylation reaction

trends in similar classes of compounds. Using one or more of the methods mentioned

above (or a novel method of your own choosing), (A) estimate the temperature at which

you would expect decarboxylation of CBDA to be thermodynamically favorable. (B)

Decarboxylation reactions in organic compounds are known to often have high activation

barriers. Hence, the thermodynamics can often be hindered by kinetics. Suggest one or

more potential catalysis to would potentially speed up this reaction.