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Biochemistry I
PS2 Recitation
September 1, 2016
1. Go to the following URL and perform a pH titration.
a) Collect data for the pH versus mls of NaOH added. Use Excel to plot your titration data.
b) Determine the pKa and the type of acid (based on the list of pKa on the web page).
https://andrew.cmu.edu/user/rule/bc_oli/Pset/PS02/titration.html
2. You are required to make a 250 ml solution of 0.05 M bis-tris to use as
R  [ A ] /[HA]  10 ( pH  pKa)
a buffer to perform a biochemical experiment at pH 6.0. You only have
f HA  1 /(1  R)  [ HA] /[ AT ]
the fully deprotonated form of this acid in the lab, plus 1M solutions of
HCl and NaOH. What additional information do you need to complete
f A  R /(1  R)  [ A ] /[ AT ]
this problem?
a) Sketch the titration curve for this buffer on the right.
b) How many moles of the deprotonated bis-tris do you need to add to make your buffer solution?
c) Does your answer to b) depend on the pH of the solution?
c) Calculate fHA and fA. Do your calculated values agree
with what you would estimate from the titration
curve?
d) How many equivalents of HCl or NaOH do you have
to add (specify what would be added to the solution)?
e) How many moles of HCl or NaOH would you have to
add?
√ Have someone check your work
3. The protein shown on the right contains one histidine
residue and one aspartic acid.
a) What would you predict for the pKa of the histidine
residue? Higher or lower than the normal pKa of
6.0? Why? [Hint: how will the negative charge
affect the acidity of the histidine?]
O
O
H
N
+
N
H
N
N
H
100
b) Assuming the protein is only biologically active when the
histidine is deprotonated, sketch the activity as a function
of pH. [Hint: Is the activity proportional to fHA or fA- ?].
What is the x-axis of this plot?
%
activity
50
0
√ Have someone check your work.
O
O
+
+
H
You will use graphical methods to
determine the net charge on the
peptide (you could use the formula for
fHA to get more accurate numbers). The
overall charge (averaged over all the
molecules) is just the weighted sum of
the charges on each group:
n
i
i
qTOTAL   ( f HA
q HA
 f Ai q iA )
i 1
Fraction Protonated
Biochemistry I
PS2 Recitation
4. A tripeptide (Ala-Ala-His) is shown to the
right, fully protonated at low pH (left) and
pKa=6
fully deprotonated at high pH (right). This
diagram indicates the charge on each
ionizable group when protonated and
deprotonated. The sidechain of histidine is
pKa=9
circled in the right diagram.
1
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
September 1, 2016
pKa=2
a) Sketch the fraction protonated versus
0 1 2 3 4 5 6 7 8 9 10 11 12
pH for each group (amino, His
pH
sidechain, carboxyl) on the graph to
the right.
b) Calculate the charge at pH = 6. Indicate the contribution of each ionizable group to the overall charge on
the diagram below. What are the predominate species in solution at this pH?
√ Have someone check your work.
5. Sketch the titration curve for the
amino acid glutamic acid, whose
structure is shown below.
a) Label the axes first,
b) add the appropriate scale, in
equivalents, on the bottom.
(One equivalent of NaOH is
equal to the number of moles
of the weak acid).
c) Indicate the buffer regions.
pKa=4
pKa=2
pKa=9.0
√ Have someone check your work.
6. View the Jmol page that shows methane and
butane dissolved in water.
a) What do the dotted purple lines represent?
b) Which of these two compounds would you
expect to be less soluble in water? Why?
c) Which of the two compounds would cause a
larger decrease in the entropy of water? Why?
√ Have someone check your work.