Chapter 3 Homework:

4, 7, 8, 9, 10, 11, 14, 20, 21, 25, 28, 29, 30, 40

4. Identify the polar, aromatic and sulfur
containing amino acids in the peptide
below:
In the peptide:

Val—Met—Ser—Ile—Phe—Arg—Cys—Tyr—
Leu,
The polar amino acids are Ser, Arg, Cys,
and Tyr;
The aromatic amino acids are Phe and Tyr;
The sulfur-containing amino acids are Met
and Cys.
7. Predict the ionized forms at pH 7:
The ionized forms of each of the
following amino acids at pH 7—glutamic
acid, leucine, threonine, histidine, and
arginine—are as follows:
8. Draw the structures of the
amino acids below at pH 4:
8.
Histidine

1.82 6.0
9.17
Structure at pH 4.0
Isoelectric point= (6.0 + 9.17)/ 2 =7.59
8. Arginine extra structure
O O O
+
2.17
H 3N CH C OH +
H 3N CH9.04
C O- H 2N CH C O-
12.48 O
H2 N CH C O-
StructureCH
at pH 4.0
CH 2

CH 2
CH
CH
CH2
2
2

Isoelectric point:CH(9.04 +CH 12.48)/2CH = 10.76

CH 2 2
CH 2
2
2 2
NH CH 2
NH NH
C NH 2+ NH
C NH 2+ C NH 2+
NH 2 C NH
NH2 NH2
NH2
8. Asparagine
2.02 8.80
Structure Oat pH 4.0 O O

Isoelectric
+
H N CH C point:
3 OH H N (2.02
+
CH C
3 O + 8.80)/2
H N CH C = 5.41
-
O 2
-

CH2 CH 2 CH2

C O C O C O

NH2 NH 2 NH2
8. Tryptophan
O 2.38
O O

9.39 +H N
CH C
3 OH H N +CH C
3 O H N
-
CH C
2 O -

Structure
CH
at pH 4.0
2 CH 2 CH 2

Isoelectric point: (2.38 + 9.39)/2 =

5.89 HN HN HN
8. Proline
O O O

C O- O-
1.99 10.96
C OH C

Structure Hat
+ N
pH 4.0
H N +
HN 2

Isoelectric point = (1.99 + 10.96)/2 = 6.49

2
8. Tyrosine

2.20 9.11
10.07
O O O O

Structure
HO C
atCHpH
NH 4.0:
O
3
+
C -
CH NH O C CH NH
3
+
O C
-
CH 2
-
NH 2

Isoelectric point:
CH2
(2.20
CH
+ 9.11)/2
2CH
= 5.67CH 2 2

OH OH OH O-
9. Predict the forms of the amino acids in
problem 8 at pH 10: Histidine imidazole is
deprotonated, α-amino group is
predominantly deprotonated. Histidine:

1.82 6.0
9.17
Structure at pH 10.0
Isoelectric point= (6.0 + 9.17)/ 2 =7.59
9. Arginine extra: Amino group is
predominantly
O deprotonated
O O
+
H 3N CH C OH +
O
H 3N CH C O- H 2N CH C O-
CH 2 H2 N CH C O-
CH2 CH2
CH2
CH 2
2.17
CH2 CH2 9.04 CH2
CH 2
12.48 CH2 CH2
CH2
NH NH
Structure CatNH pH 10.0:
C NH 2
+
C NH
NH
2
+
NH

2
+
C NH
Isoelectric point: (9.04 + 12.48)/2 =
NH NH 2
NH
NH 10.76
2 2
2
9. Asparagine: α-amino group is
deprotonated.
2.02 O
8.80
O O
Structure
+
H N CH C
atOHpHH N 10.0
+
CH C O H N CH C O- -
2

Isoelectric point: (2.02 + 8.80)/2 = 5.41

3 3

CH2 CH 2 CH 2

C O C O C O

NH2 NH 2 NH2
9. Tryptophan: α-amino group is
predominantly deprotonated.
O O
+H N
2.38 9.39 O
CH C OH +H O-
Structure at pH 10.0
-
3 H N 3N
CH C O CH C 2
CH 2 CH CH 2

Isoelectric point: (2.38 + 9.39)/2 =

2

5.89 HN HN HN
9. Proline: α-amino group is partially
deprotonated.
O O O

C OH C 1.99
O- C O- 10.96
Structure at pH 10.0
Isoelectric point
+H N2
= (1.99
H N + 10.96)/2
+
HN
2
= 6.49
9. Tyrosine: α-amino group is predominantly
deprotonated, phenolic hydroxyl is
approximately a 50–50 mixture of protonated
and deprotonated forms.
O O O O

HO C CH NH3 + -O
C CH 2.20
NH 3+-
O C CH NH2 -
O 9.11
C CH NH2

10.07
CH 2 CH2 CH 2 CH 2
Structure at pH 10.0:
Isoelectric point: (2.20 + 9.11)/2 = 5.66

OH OH OH O-
10. Calculate the isoelectric point of the
following amino acids:
Glutamic acid
2.19 4.25 9.67
Isoelectric point: (2.19 + 4.25)/2
=3.22
O O O
O
+
+H N H3 N CH C O- H 2N CH C O- +H N
3 CH C OH
3 CH C OH
CH 2 CH2 CH 2
CH2
CH 2 CH2 CH 2
CH2
C O C O C O
C O
OH O-
OH O-
10. Serine
2.21
9.15
Isoelectric point = (2.21 + 9.15)/2=
5.68
O O O

H 3N CH C OH H3 N CH C O- H 2N CH C O-

CH2 CH 2 CH2

OH OH OH
10. Histidine
1.82
6.0 9.17
Isoelectric point: (6.0 + 9.17)/2
=7.59
10. Lysine:
2.18 8.95 10.53

O O O O
+ +H
H 3N CH C OH 3N CH C O- H 2N CH C O- H 2N CH C O-
CH2 CH 2 CH 2 CH 2
CH2 CH 2 CH 2 CH 2
CH2 CH 2 CH 2 CH 2

CH2 CH 2 CH 2 CH 2

NH3 + NH 3+ NH 3 + NH 2

Isoelectric point : (8.95 +

10.53)/2 = 9.74
10. Tyrosine
2.20 9.11 10.07
O O O

Isoelectric point: (2.2 +

O
+
+H N H3 N CH C O- H 2N CH C O- +H N
3 CH C OH
3 CH C OH
CH 2 CH2 CH 2

(9.11)/2= 5.66
CH2
CH 2 CH2 CH 2
CH2
C O C O C O
C O
OH O-
OH O-
10. Arginine:
O O O
+
H 3N CH C OH + -
O
H 3N CH C O H 2N CH C O-
CH 2 H2 N CH C O-
CH2
Isoelectric point:
CH 2 (9.04 + 12.48)/2
CH
= 10.76
CH2
CH2
2 CH2
CH 2 CH2

NH
2.1 CH2
9.0 CH2 12. CH2
NH
C NH 2+ 7 C NH +
4 NH
48 NH
2 C NH 2+
NH 2 C NH
NH2 NH2
NH2
11. Sketch a titration curve for cysteine. Indicate
pKs and pH at which there is no net charge
Cysteine has no net charge at pH 5.08 = (1.96 +
8.18)/2 (see titration curve below).
8.18 10.28
11

pI=5.08
1.96

K2
K3
14. Sketch the titration curve for aspartic
acid. Indicate pK vales. At what pH will
the acid-base pair +1 Asp and 0 Asp act
as a buffer? The conjugate acid–base pair acts
as a buffer in the pH range 0.9–2.9.

9.60

3.65
1.88

pI 2.77
20. Identify the charged groups in the peptide
shown below at pH 1 and pH 7. What is the
net charge at these two values
Amino
Carboxy
Terminus Terminus
Val—Met—Ser—Ile—Phe—Arg—Cys—Tyr—Leu
9.62 12.48 8.18 10.07
2.36
+1 +1 0 0 0

Total =+2
+1 +1 0 0 atpH = -1
1.0
Total +1
at
pH = 7.0
21. Identify the charged groups in the peptides
shown below at pH 1 and pH 7. What is the net
charge at these two values?
Amino Carboxy
Terminus Terminus
9.13 4.25 2.28
+1 Phe—Glu—Ser—Met
0 0 Net charge at
pH 1.0= +1 Val—Trp—Cys—Leu
+1 -1 -1 Net charge at
pH 7.0 = -1
9.62 8.18 2.36
+1 0 0 Net charge at pH
1.0 = +1
+1 0 -1 Net charge at pH
7.0 = 0
25. How do the resonance
structures of the peptide group
contribute to the planar
arrangement of this group of
atoms?
The resonance structures contribute
to the planar arrangement by giving
the CON bond partial double-bond
character.
28.Consider the peptides
below. How do they differ?
Ser-Glu-Gly-His-Ala
Gly-His-Ala-Glu-Ser
The two peptides differ in
amino acid sequence but not
in composition.
29. Would the titration curves of the
peptides in question 28 differ? Why?
The titration curves of the two peptides
have the same general shape. The pKa
values of the α-amino and α-carboxyl
groups differ. Very careful work will show
slight differences in side-chain pKavalues
because of the different distances to the
charged groups at the ends of the peptide.
Such changes are particularly marked in
proteins.
Ser-Glu-Gly-His-Ala
Gly-His-Ala-Glu-Ser
1.What are the sequences of all
tripeptides that contain
Asp, Leu and Phe?
Asp—Leu—Phe
Leu—Asp—Phe
Phe—Asp—Leu
Asp—Phe—Leu
Leu—Phe—Asp
Phe—Leu—Asp
40. Can you separate the peptides in
question 39 (shown below) by
electrophoresis?
Gly-Pro-Ser-Glu-Thr open chain
Gly-Pro-Ser-Glu-Thr with a peptide bond
linking Thr and Gly (this forms a cyclic
peptide)
Both the C-terminal and the N-terminal
of the open-chain peptide can be
charged at appropriate pH values, which
is not the case with the cyclic peptide.
This can provide a basis for separation
by electrophoresis.