Chemistry 122 Exam 2

February 26, 2009

NAME: ___________________
please PRINT!

ALL ANSWERS MUST GO ONTO THE ANSWER SHEET

RETURN THIS INTO THE EXAM BOX EVEN THOUGH ONLY THE
ANSWER SHEET WILL BE GRADED

**Notes**
• Potentially useful equations can be found on the last page
• THINK BEFORE YOU CALCULATE!
- Some quantitative problems can be solved without calculations.
- You may run out of time if you calculate unnecessarily
• Don’t forget to provide units and label axes, etc.!
• PLEASE PUT ALL WORK ON THE SECOND-THIRD PAGES OF THE ANSWER SHEET,
clearly labeled as to which problem it belongs to.

• Every answer is 2 points!

ANSWER THE EASY QUESTIONS FIRST

• You may start as soon as you have everything put away
1. For the following, choose the best (most specific) answer from the following list:

antigen myoglobin Immunofluoresce ELISA

ligand porphyrin nce exergonic
antibody(s) western blot NMR exothermic
MHC molecule(s) Southern blot X-ray enthalpic
hemoglobin Northern blot crystallgraphy endothermic

a) Proteins that are on the surface of cells and present to the immune system pieces of what is inside;
these proteins must be properly matched between donors and acceptors if organ transplants are to be
successful _________
b) Appropriate technique to localize where a particular protein is on an SDS gel _________
c) Appropriate technique to localize a particular protein inside a cell ________
d) heme is an example of a(n) ________
e) Vaccines work by causing your body to produce ________ against particular pathogens, thus
protecting you from future infection.
f) Autoimmune diseases occur when your body produces ________ against your own proteins
g) A(n) _______ reaction is one that has a negative delta G

2. Understanding equilibrium constants. A+B AB

Consider the following reaction (see A + B at right):
a) Give the equation for the Kd in terms of concentrations (i.e., Kd = ???)
b) Give the equation for the relationship between Ka and Kd
c) Give the equation for the Kd in terms of the rate constants
(note: if you are not sure, THINK about it – this should not be a memorization question)

3. Give an example of a heterotropic allosteric modulator of hemoglobin

4. Understanding the effects of enzymes.

Imagine that the hypothetical reaction A -> B occurs with a rate k in the absence of an enzyme.
For each of the following quantities, state on the corresponding line whether its value would be
“increased” “decreased” or “unchanged” (relative to the uncatalyzed reaction) if an enzyme that
catalyzes the reaction is added.
Note that this should not be a “memorization” question – if it helps you, draw a diagram, but you will
not be given credit for the diagram.
a) standard free energy ∆G°
b) transition state energy ∆G‡
c) k1 (the forward rate constant)
d) K (the equilibrium constant)
e) the amount of product achieved at equilibrium
f) the amount of time that it takes to get to equilibrium
g) the amount of product produced in a given amount of time
/36
5. Enzyme Kinetics

Carbon dioxide reacts with water to produce biocarbonate and hydrogen ion
CO2 + H20 -> HCO3- + H+
(this is the reason that even pristine rain is somewhat acidic) CO2
concentration Reaction velocity
In your body, an enzyme called carbonic anhydrase catalyzes (mmol/L) (mmol/(sec*L)
this reaction, allowing CO2 to be removed in your blood. A 0.25 40.00
study of the kinetics of carbonic anhydrase found the 0.5 66.67
following results (table at right): 0.75 85.71
1 100.00
2 133.33
For the following four problems, answers within 10% are 5 166.67
10 181.82
acceptable
30 193.55
a) What is Vmax?
60 196.08
b) What is Km? 120 200.00
c) What would the velocity be when [CO2] = 240mmol/L?
d) What would the velocity be if the amount of enzyme was doubled when [CO2] = 60?
e) When you doubled the enzyme in part d, did the Km change?

For the next three problems, show your work by at the bottom of the answer sheet.
Be careful to include any equations and values used to figure out the answers
f) What would the velocity be when [CO2] = 7.5mmol/L?
(this number must be within 1%;)

g) Assume that the concentration of enzyme is 10µM. What is kcat?

h) On average, how much time does it take one molecule of carbonic anhydrase to catalyze one
reaction?

6. Interpreting graphs of protein-ligand interactions

Assume that all of the following graphs have θ on the Y axis and [ligand] on the X axis
For each, chose the most appropriate description: “simple”, “cooperative,” “you can’t tell for
sure,” or “these cannot be plots of protein-ligand interactions” (short version: “can’t be PL”)

A B C

7. Interpreting enzyme kinetics graphs

Now imagine that these same plots are for enzyme-catalyzed reactions with “Initial Velocity” on the Y
axis and [substrate] on the X axis.
For each, chose the most appropriate description: “simple”, “cooperative,” “you can’t tell for
sure,” or “these cannot be plots of enzyme catalyzed reactions” (short version: “can’t be EC”)

/26
Ligand binding
You are studying obesity, and have identified a pair of interacting proteins involved in the response of
the body to food: Protein A is a kinase involved in signaling hunger, and protein B binds to it. When
protein A is active, you are hungry, but binding of B to A inhibits the kinase activity and so prevents
the feeling of hunger.

You have decided to study this interaction in more detail so that you can ascertain whether protein B
might be developed as a diet-aid. A key aspect of this characterization is to determine the Kd.
You have done the following experiments (see below)
please give correct interpretation by choosing from these possible answers:

For Kd values, choices are: For percent binding problems, choices are:
(these must be good to within 10%) (Choose whichever is closest to the real value)
• 1nM • <1%
• 1µM, • ~25%
• 1mM • ~50%
• can’t tell; need more information or another • ~75%
experiment to achieve accuracy within 10% • >90%
(“can’t tell” is sufficient for the answer box)

8. You have 1nM protein A and you mix it with 1µM protein B. You find that half of the protein A
has protein B bound to it.
a) what fraction of protein B has protein A bound to it?
b) what is the Kd for the A-B interaction?

9) You find that protein B has a relative “Protein C” that also inhibits protein A (and so also prevents
the feeling of hunger), but it turns out that this protein is very hard to purify. Therefore, when you
do the binding assay, you have very little of it. You mix 1nM protein A with 0.5nM protein C, and
find that half of the protein A has protein C bound to it.
a) What fraction of protein C has protein A bound to it?
b) What is the Kd for the A-C interaction?

10) In separate studies you find out that in humans, serious side effects start to occur at 1µM of either
protein, but 10nM concentrations are tolerated well. Given this information, which of the
following is true?
a) protein A has more potential as as a diet-aid drug
b) protein B has more potential as as a diet-aid drug
c) Both A and B are equally likely to work
d) Based on this information, neither A nor B could work

Note: you can use the space below for scratch paper, but any calculations that are important to your
answer should go carefully labeled onto the second page of the answer sheet

/26
11. Multiple Choice
a) Imagine that you are a chemical engineer working for a pharmaceutical company, and you’ve been
been assigned the task of designing a new antibiotic that kills bacteria by binding to and inhibiting a
bacteria-specific enzyme. Which of the following would likely yield the best inhibitor? (Assume
that manufacture of all of these compounds is equally practical; for the purposes of this problem,
assume that the “best” inhibitor is the one that inhibits the enzyme at the lowest inhibitor
concentration).
a) design a compound that looks like the substrate of the reaction but cannot be broken down
b) design a compound that looks like the transition state of the reaction but cannot be broken down
c) design a compound that looks like the product but cannot participate in the reverse reaction
d) none of the above would be likely to inhibit the enzyme

b) Which of the following better describes the manner in which enzymes bind substrates?
a) “lock and key”
b) “induced fit”
c) “heterotropic allosteric modulation”
d) “homotropic allosteric modulation”

c) Which of the following is not a mechanism use to regulate protein function and/or activity?
a) phosphorylation
b) proteolysis
c) change of localization
d) all are mechanism used to control protein activity
e) none are mechanisms used to regulate protein function and/or activity

d) You have four related but different ligands that all bind to the same protein. They bind with the
following Kd values. Which of the following Kd values corresponds to the highest affinity?
a) 1mM
b) 10mM
c) this question is meaningless – affinity is measured by Ka
d) you can’t compare affinities of different ligands for the same protein

e) Explain why CO binds to heme in hemoglobin less strongly than it binds to naked heme
a) the cooperativity of hemoglobin interferes with CO binding
b) the steric constraints imposed by the protein surrounding the heme force the CO to bind at an angle
c) the statement is incorrect – CO binds to heme in hemoglobin more strongly than it binds to naked
heme
d) The heme in hemoglobin has iron, while free heme has magnesium

f) Consider the following balanced chemical reaction: 2A + B -> C.

What order is this reaction with respect to A?
a) 0th
b) 1st
c) 2nd
d) can’t tell without doing an experiment

/8
g) Which of the following statements about enzymes is correct?
a) enzymes can sometimes become temporarily covalently attached to their substrates
b) enzymes can change the path of a reaction
c) enzymes can be made of RNA
d) all of the above are correct

h) Why don’t bags of sugar (and people) “spontaneously combust?”

a) the activation energy is too high
b) the free energy change for combustion is positive
c) the entropy change is too great
d) The Km is too high
e) They do… it just happens very briefly

i) Which of the following curve shapes more accurately represents the relationships between
chemical rate constant and the temperature for a generic chemical reaction in relevant temperature
ranges? (the equation for the rate constant can be found on the last page)
A B C D

temperature

THE EXAM CONTINUES!

Very short essays: These are listed on the second side of the answer sheet

PLEASE DON’T FORGET TO DO THESE!!

/8
Notes: M is the abbreviation for molar; mol is the abbreviation for moles