Chemistry 160 Exam 2 key
Please put your name on this exam. Be sure to answer all of the questions as
completely as possible. There is some useful information on the last page.
100 points
(10) 1. For each of the following, give an amino acid that has a side chain that fits the
description.
a. Primary alcohol Serine
b. Thiol cysteine
c. Doesn’t fit into an α-helix proline
d. Deprotonated at physiological pH aspartate, glutamate
e. Amide asparagines, glutamine
f. Phenol side chain tyrosine
g. Part of aspartame phenylalanine, aspartate
h. Nonpolar phenylalanine, tryptophan, methionine, glycine, valine, leucine, isoleucine
i. Positively charged at physiological pH histidine, arginine, lysine
j. Smallest amino acid glycine
(5) 2. Describe isoelectric focusing and how it can be used to separate a mixture of amino acids.
Amino acids are placed in a gel that has a pH gradient. An electric field is applied and amino
acids move towards either the positive or negative side depending on their charges. As they
move through the gel they are protonated or deprotonated depending on the pH. Eventually they
get to their isoelectric point (where there is no net charge) and no longer move through the gel.
Separates by isoelectric point.
Chemistry 160 Exam 2 Key Pg. 2
(10) 3. Show the structure of aspartate at the following pH’s
O
O
H3N+
H3N+
OH
O
O
O
b. 3.55
O
c. 7.00
O
H2N
O
O
O
O
O
d. 9.00
O
OH
O
H3N+
H3N+
O
OH
a. 1.05
O
O
e. 11.00
(5) 4. Show, using Lewis dot structures, why there is no free rotation around a peptide bond.
-
O
O
H3N+
N
H
R1
O
O
H3N+
R2
O
O
H3N+
NH
O
O
NH
O
NH
O
O
NH
H2N+
NH2
NH3+
O
N
R1
(10) 5. Draw the peptide (D-A-R-K) at pH 9.55
O
+
R2
Chemistry 160 Exam 2 Key Pg. 3
(10) 6. Describe the 4 levels of protein structure.
Primary = amino acid sequence
Secondary = simple folding like α helix or beta sheet
Supersecondary = patterns of secondary
Tertiary = 3 D structure
Quaternary = subunit interactions
(5) 7. Give two types of forces that hold proteins in their 3-D shape. Draw a diagram for each.
R
O
O
N
- -- -- -- -- H3N+
O
O
R
R
R
N
electrostatic interactions
R
R
O
N
R
O
H
O
N
H
R
O
hydrogen bonding
(10) 8. When peptides are made in a test tube, it is done solid phase.
a. Briefly describe the process by which it is done.
They are made in reverse order. An amino acid with the side chain and amino group chemically
blocked is attached to a solid bead. The blocking group is removed from the amino and the
mixture is washed and filtered. The next amino acid, with side chain and amino blocked (also
activated carboxyl) is added and a peptide bond is formed. The mixture is then washed and
filtered to remove excess. The process is then repeated until the desired sequence is made. The
blocking groups are removed from the side chains and the mixture is washed and filtered.
Finally the peptide is removed from the bead.
b. Why is this method such an advantage over synthesis in solution?
If this is done in solution the purification steps at each stage are tedious and low yield. In this
situation, the purification is by filtration.
Chemistry 160 Exam 2 Key Pg. 4
(5) 9. What do we mean when we say, “peptides are vectorial”?
There is a direction…different ends (an amino and a carboxyl end)
(5) 10. What is the induced fit model of protein-ligand binding? How does it differ from lock
and key?
The lock and key hypothesis has complementary shapes that are rigid for protein and
ligand. In the induced fit model, the shapes are somewhat complementary, however the shapes
change upon binding and then the complementarity is achieved.
(5) 11. Give three roles of proteins.
Regulatory: hormones
Enzymes
Structural
nutritional
(5) 12. During purification of an enzyme, we frequently monitor specific activity. What is
specific activity and how can we use it to determine enzyme purity?
Specific activity is activity/mg protein. During a purification process as we remove “junk”
protein, the specific activity should increase. When a protein is pure, additional steps should not
change specific activity.
(5) 13. Enzymes provide activation energy for reactions. Give three ways they do this.
Binding forces substrate into unstable intermediate state (induced fit)
Release of water of hydration (hydration shells around nonpolar amino acids) during binding
increases entropy of surroundings
Binding brings reactive groups together
Chemistry 160 Exam 2 Key Pg. 5
(5) 14. What is the purpose of studying enzyme kinetics? (What information do we get from it?)
To determine mechanism
(5) 15. Draw a cartoon diagram of an enzyme showing allosteric inhibition. Describe your
drawing.
Binding of the inhibitor (triangle) changes shape of the active site so substrate doesn’t bind so well.
Chemistry 160 Exam 2 Key Pg. 6
Useful Information
O
pK = 9.04
H3N+
pK = 2.17
O
O
pK = 9.82
H3N+
O
pK = 2.09
NH
O
O
H2N+
NH2
pK = 12.48
pK = 3.86
Aspartate (D)
Arginine (R)
O
H3N+
pK = 8.95
O
pK = 2.18
O
pK = 9.69 H3N+
O
Alanine (A)
pK = 2.34
NH3+
Lysine (K)
pK = 10.53