Student Name______________________

BIOCHEMISTRY I
HOMEWORK I
DUE 9/15/03
59 points total

The answers are given in bold font.

For problems in which points were assigned for different parts, the breakdown of
points are given in red for the associated parts.

Average = 46 ± 6 points
 Student Name______________________
BIOCHEMISTRY I
HOMEWORK I
DUE 9/15/03
59 points total

1). 9 points total

Fill in the table: For each of the following modified amino acid side chains, identify the
parent amino acid from which it was derived by its one-letter code, the chemical
classification of the parent amino acid and the type of chemical modification that has
occurred.

Under modifications, I was looking for the name of the chemical modification.

Modified Residue One letter Chemical classification of Modification

code parent amino acid
-CH2OPO3- S polar, uncharged phosphorylation
-CH2CH-(COO-)2 E polar, charged (negative) carboxylation of γ-
carbon
-(CH2)4-NH-C(O)CH3 K polar charged (positive) acetylation of ε-amino
group

2). 20 points total

T or F (2 points each; if false, briefly state why it is false).

_____The three-dimensional structures of biomolecules combine the properties of

flexibility and stability (T).

_____The term "hydrophobic interactions" describes the tendency of hydrophobic

groups to sequester away from H20. T

_____Osmotic pressure is the amount of pressure required to prevent the net movement
of solute from one side of a semi-permeable membrane to another. False - prevents the
net movement of water,not solute.

_____Weak acids are completely ionized in H20. (false - partially ionized).

 Student Name______________________
_____A reaction with ∆G = - 10 kcal/mol will occur more rapidly than one with a ∆G = -5
kcal/mol. False - thermodynamics tells us whether a reaction will go, not how fast
it will go.

_____Free energy change is a constant for a reaction under any condition. False - Free
energy change is very dependent upon conditions! e.g., ∆G = -RTlnK

_____Histidine provides the major buffering action of proteins at physiological pH

values T

_____At pH 7.0, the net charge on the amino acid lysine is +2 (False; +1)

_____Covalent bonds between amino acids are primarily found as two types - the peptide
bond and the disulfide bond. True

_____Amino acids can never have four different protonation or ionization states. False
- see page 77.

Problem Solving and Short Answer Questions

Short answers - short answers consist of no more than 5 sentences!

3). 2 points
Why are living organisms open systems, i.e., why is the cell membrane not an absolute
barrier between the cytoplasm and the external environment? The short answer is that
cell membranes must be semi-permeable to permit nutrients to enter and wastes to
exit.

4). 7 points total

Aspirin is a weak acid with an ionizable carboxyl group with a pKa = 3.5. The structure is
drawn below.
A. Circle the ionizable hydrogen in the structure below.
+1 point for this
 Student Name______________________

Question 4 continued:

Aspirin functions by being absorbed through the cells lining in the stomach and small
intestine. Absorption requires passage through a plasma membrane, which is hydrophobic.
It makes sense then, that the rate of passage is determined by the polarity of the
molecule: charged and highly polar molecules pass slowly, whereas neutral hydrophobic
ones pass rapidly. The pH of the stomach contents is about 2, and the pH of the
contents of the small intestine is about 5.

B). Calculate the percentage of the un-ionized form of aspirin at pH 2 and pH 5.

For pH 2:

i). Use the Henderson - Hasselbach equation:

pH = pKa + log [RCOO-]/[RCOOH] +1 point for using Henderson-
Hasellbach equation
2=3.5 + log[RCOO-]/[RCOOH]
[RCOO-]/[RCOOH] = .032 or a molar ratio of .032 to 1 +1 point

ii). Calculate percentage of uncharged species is the concentration of that species

over the total concentration of all species:
%RCOOH = [RCOOH]/([RCOO-]+[RCOOH]}

%RCOOH = 1/(1+.032) = 97% +1 point

For pH 5: RCOO-]/[RCOOH] = 32 or a molar ratio of 32 to 1 +1 point

%RCOOH = 3% +1 point

C). Based on your answer above, is more aspirin absorbed into the bloodstream from the
stomach or small intestine?

Stomach. +1 point
 Student Name______________________
5). 2 points total
Osmotic lysis is a gentle method of breaking open animal cells to free intracellular
proteins. In this technique, cells are suspended in a solution that has a total molar
concentration of solutes much less than that found naturally inside cells. Explain why this
technique might cause cells to burst.

There is a larger osmotic pressure inside the cells than outside because the molar
concentration of solutes is much greater inside cells than outside. This results in a
diffusion of water into the cells (in an attempt to equalize the concentrations of
solutes on both sides of the membrane) causing the cells to swell and burst.

6). 2 points total

When a hydrophobic substance like a hydrocarbon is dissolved in water, a clathrate cage
of ordered water molecules is formed about it. What do you expect the sign of ∆S to be
for this process? Explain your answer.

This process would correspond to an entropy decrease (∆S < 0) because order is
being established in the H2O structure.
 Student Name______________________

7). 6 points
For the reaction HC2H3O2 !" C2H3O2- + H+, calculate ∆Go and ∆Go'. Assume T = 25C.
The ionization constant for acetic acid is 1.8 x 10-5. Is this reaction spontaneous at 25C?

i). Keq = ([C2H3O2-][H+])/[HC2H3O2]

∆Go = -RTln Keq +1 point note R = 8.314 J/mol-K and

T= 25o+273.15
In a plug and chug

∆Go = +27.1 kJ/mol +1 point

A positive value of ∆Go indicates this reaction is not spontaneous under standard
conditions. +1 point

ii). ∆Go' = ∆Go + RTln [H+] +1 point

= +27.1 kJ/mol + RTln [H+]

= 27.1 + (8.314)(298) ln (1 x 10-7)

= -12.8 kJ/mol +1 point

At pH 7.0, this reaction is spontaneous +1 point

 Student Name______________________
8). 4 points total
A peptide has the sequence Glu-His-Trp-Ser-Gly-Leu-Arg-Pro-Gly

A). Write this peptide using one letter code.

E-H-W-S-G-L-R-P-G +1 point

B). What is the net charge of the molecule at pH 3? At pH 8?

Write the pKas for all the ionizable groups - don't forget the amino and carboxyl
termini! Figure out the charge on each group at each pH value based on their pKas.
Remember, if the pH is below the pKa, the group is protonated!

+
H3 N E H W S G L R P G COO-
terminus terminus
pKa 9.7 4. 6 12.5 2.0
3
Charge +1 0 +1 - - - - +1 - - -1
at
pH 3.0
Charge +1 -1 0 - - - - +1 - - -1
at
pH 8.0

pH 3: +2 +1 point
pH 8: 0 +1 point

C). Estimate the pI for this peptide.

You need to figure out the pH range where the molecule would have a net charge of
0. Based on the above table, this is between pH 6 and pH 9.7. The pI is then the
midpoint of the range or

pI = (6+9.7)/2 = 7.85 +1 point

 Student Name______________________
9). 7 points total
Ramachandran plot: The following two Ramachandran plots represent permitted values of
ψφ for different amino acids.

A). What do the values of ψφ represent?

ψ = permitted rotation about the Cα-CO bond +1 point

φ = permitted rotation about the Cα-NH bond +1 point
B). Put a G on the line under the plot that best represents the ψφ space for glycine. Put
an L on the line under the plot that best represents the ψφ space for leucine. +2 point

C).On the appropriate plot:

Mark a B on the region where we would expect to find amino acids in beta sheet
structures.
Mark an A on the region where we would expect to find amino acids in alpha-helical
structures.

___L___ ___G__

The most appropriate plot that shows any type of significant structure is the plot
for leucine. The B would go in the upper left corner where there is a high density
of points. The A would go in the central left side where there is a high density of
points. +2 point

D). Would you expect proline to occupy more ψ−φ space than alanine - why or why not?
No, due to its restricted backbone conformation, it would not. +1 point