Download AMINO ACIDS, POLYPEPTIDES, AND PROTEINS

CHAPTER 29
AMINO ACIDS, POLYPEPTIDES, AND PROTEINS
SOLUTIONS TO REVIEW QUESTIONS
1.
The designation, α, means that the amine group in common amino acids is connected to
the carbon immediately adjacent to the carboxylic acid. The designation, L, means that
the common amino acids all have a specific configuration around the α-carbon. The
amine group is on the left when the amino acids are written in a standard Fischer
projection formula.
2.
CH3 CH2
CH
CH
CH3
NH2
COOH
H2 N (C H2 )4 CH
COOH
NH2
K, lysine
I, isoleucine
3.
The amino acid, lysine (K), has a pH of 9.7 at its isoelectric point. This pH fits into the
range of 7.8 to 10.8 found for basic amino acids.
4.
The zwitterion form of isoleucine (I) follows:
CH3CH2
CH
CH
CH3
NH3
–
COO
+
This is a zwitterion because the compound is ionized but the charges cancel so that the
overall charge is zero.
5.
Amino acids are amphoteric because the carboxyl group can react with a base to form a
salt, or the amine group can react with an acid to form a salt. They are optically active
because the alpha carbon is chiral, except for glycine. They commonly have the L
configuration at carbon two, as in L-serine.
6.
At its isoelectric point, a protein molecule must have an equal number of positive and
negative charges.
7.
(a)
(b)
Primary structure. The number, kind, and sequence of amino acid units comprising
the polypeptide chain making up a molecule.
Secondary structure. Regular three-dimensional structure held together by the
hydrogen bonding between the oxygen of C O groups and the hydrogen of the
N ¬ H groups in the polypeptide chains.
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(c)
(d)
Tertiary structure. The distinctive and characteristic three-dimensional
conformation or shape of a protein molecule.
Quaternary structure. The three-dimensional shape formed by an aggregate of
protein subunits found in some complex proteins.
8.
The sulfur-containing amino acid, cysteine, has the special role in protein structure of
creating disulfide bonding between polypeptide chains which helps control the shape of
the molecule.
9.
Collagen is a good structural protein because its three-dimensional structure is held
together strongly. Three protein strands are coiled in left-handed helices and then
wrapped together in a right-handed helix. This cable construction resists stretching.
10.
Ferritin is a good iron storage protein because its three-dimensional structure provides a
sack for holding iron atoms. This protein is made up of many subunits that together form
a hollow sphere (a quaternary structure) within which the iron is stored.
11.
Hydrolysis breaks the peptide bonds, thus disrupting the primary structure of the protein.
Denaturation involves alteration or disruption of the secondary, tertiary, or quaternary but
not of the primary structure of proteins.
12.
Amino acids containing a benzene ring give a positive xanthoproteic test (formation of
yellow-colored reaction products). Among the common amino acids, these would include
phenylalanine, tryptophan, and tyrosine.
13.
The visible evidence observed in the:
(a) Xanthoproteic test gives a yellow-colored reaction product when a protein
containing a benzene ring is reacted with concentrated nitric acid.
(b) Biuret test gives a violet color when dilute
is added to an alkaline solution
of a peptide or a protein.
(c) Ninhydrin test gives a blue solution with all amino acids except proline and
hydroxyproline, both of which produce a yellow solution when ninhydrin is added
to an amino acid.
(d) In the Lowry Assay test a dark violet-blue color is produced when a protein
contains tyrosine and tryptophan amino acids.
(e) In the Bradford Assay test a deep blue color develops when a protein binds to the
dye Coomassie Brilliant Blue.
14.
Protein column chromatography uses a column packed with polymer beads (solid phase)
through which a protein solution (liquid phase) is passed. Proteins separate based on
differences in how they react with the solid phase. The proteins move through the column
at different rates and can be collected separately.
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15.
(a)
(b)
(c)
16.
Thin layer chromatography is a way of separating substances based on a differential
distribution between two phases, the liquid phase and the solid phase.
A strip (or sheet) is prepared with a thin coating (layer) of dried alumina or other
adsorbent. A tiny spot of solution containing a mixture of amino acids is placed
near the bottom of the strip. After the spot dries, the bottom edge of the strip is
placed in a suitable solvent. The solvent ascends in the strip, carrying the different
amino acids upwards at different rates. When the solvent front nears the top, the
strip is removed from the solvent and dried.
Ninhydrin is the reagent used to locate the different amino acids on the strip.
In ordinary electrophoresis the rate of movement of a protein depends on its charge and
size. In SDS electrophoresis a detergent, sodium dodecyl sulfate, is added to the protein
solution, which masks the differences in protein charges, leaving the separation primarily
due to the size of the various proteins.
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SOLUTIONS TO EXERCISES
1.
COOH
COOH
H2 N
C
C
H
H
NH2
CH2 OH
CH2 OH
L-serine
D-serine
The primary alcohol group causes serine to be hydrophilic and, thus, this amino acid
prefers to be on the surface of proteins where it can interact with water.
2.
COOH
NH2 C
COOH
H
H
CH2
C
NH2
CH2
D-phenylalanine
L-phenylalanine
The benzene ring causes phenylalanine to be hydrophobic and, thus, this amino acid
prefers to be inside proteins and away from water.
3.
Basic. The amine functional group allows the amino acid side chain to accept a proton
under physiological conditions (pH of about 7). Thus, this amino acid would be classed
as basic and also as “positively-charged.”
4.
Polar, uncharged. The amide functional group causes the amino acid side chain to be
polar but uncharged.
5.
Pro = proline
–
+
NH2
COO
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6.
Gln = glutamine.
O
–
NH2CCH2CH2CHCOO
+
N H3
7.
For phenylalanine:
(a) zwitterion formula
(b) formula in
CH2CHCOO–
ƒ
NH 3±
8.
For tryptophan:
(a) zwitterion formula
(b) formula in
C
2
(c) formula in 0.1 M NaOH
4
CH2CHCOO–
ƒ
NH 2
N
H
H
NHCH2CH2CH2CHCOOH + CH3
CHCOOH
NH2
NH2
NH
O
H2N
CH2CHCOO–
ƒ
NH 2
CH2CHCOOH
ƒ
NH 3±
N
H
H2N
(c) formula in 0.1 M NaOH
4
CH2CHCOOH
ƒ
NH 3±
CH2CHCOO–
ƒ
NH 3±
N
9.
2
C
CH3
NHCH2CH2CH2CHCNHCHCOOH
NH2
NH
CH3
OH
10.
O
CHOH
CH2COOH + CH3CHCHCOOH
CH2CNHCHCOOH + H2O
NH2
NH2
NH2
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11.
At a very acidic pH, the dipeptide will carry two positive charges. The amine end of the
dipeptide and the side chain of the arginine will be protonated.
O
H2N
NHCH2CH2CH2CHCNHCHCOOH
C
+
+
NH2
12.
CH3
NH3
At a very basic pH, the carboxyl end of the dipeptide will lose a proton and will carry a
negative charge.
CH3
O
CHOH
–
CH2CNHCHCOO
NH2
13.
The two dipeptides containing serine and alanine:
CH 2OH
CH 3
CH 3
CH 2OH
ƒ
ƒ
ƒ
ƒ
NH 2CHC ¬⁄ NHCHCOOH
NH 2CHC ¬⁄ NHCHCOOH
‘
‘
O
O
peptide bond
peptide bond
Ser-Ala
14.
Ala-Ser
The two dipeptides containing glycine and threonine:
CH 3
CH 3
ƒ
ƒ
CHOH
CHOH
ƒ
ƒ
NH 2CH 2C ¬ NHCHCOOH
NH 2CHC ¬ NHCH 2COOH
‘ ⁄
‘ ⁄
O
O
peptide bond
peptide bond
Gly-Thr
Thr-Gly
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H2
C
15.
H2C
H2
C
H2C
CH2
HN
CH ¬ COOH
HN
O H2C
‘
CH¬¬ C ¬¬¬ N
CH2
Pro
16.
(b)
(c)
18.
(a)
(b)
(c)
CH¬¬ COOH
CH 2 ¬¬¬¬ S¬
¬¬ S ¬¬¬¬ CH 2
ƒ
ƒ
H 2N ¬ CH ¬ COOH
H 2N ¬ CH ¬ COOH
CH 2SH
ƒ
H 2N ¬ CH ¬ COOH
(a)
CH2
Pro-Pro
Cys
17.
H2
C
Cys-Cys
NH 2CH 2C ¬ NHCH 2COOH
‘
O
glycylglycine
alanylglycylserine
CH 3
CH 2OH
ƒ
ƒ
NH 2CHC ¬ NHCH 2C ¬ NHCHCOOH
‘
‘
O
O
glycylserylglycine
CH 2OH
ƒ
NH 2CH 2C ¬ NHCHC ¬ NHCH 2COOH
‘
‘
O
O
alanylalanine
CH 3
CH 3
ƒ
ƒ
NH 2CHC ¬ NHCHCOOH
‘
O
serylglycylglycine
C H 2O H
ƒ
NH 2CHC ¬ NHCH 2C ¬ NHCH 2COOH
‘
‘
O
O
serylglycylalanine
CH 2OH
CH 3
ƒ
ƒ
NH 2CHC ¬ NHCH 2C ¬ NHCHCOOH
‘
‘
O
O
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19.
All the possible tripeptides containing one unit each of glycine, phenylalanine, and leucine:
GFL
GLF
FGL
FLG
LGF
LFG
20.
All the possible tripeptides containing one unit each of tyrosine, aspartic acid, and alanine:
YDA
YAD
DYA
DAY
AYD
ADY
21.
H O
CH3
ƒ
‘
ƒ
¬C¬C¬N¬C¬
ƒ
ƒ
ƒ
H
H H
22.
H O
CH3
ƒ
‘
ƒ
¬C¬C¬N¬C¬
ƒ
ƒ
ƒ
H
H H
23.
Tertiary protein structure is usually held together by bonds between amino acid side chains.
Serine side chains will hydrogen bond to each other:
H
ƒ
.....
¬ CH 2O ¬ H ⁄ OCH 2 ¬
hydrogen bond
24.
Tertiary protein structure is usually held together by bonds between amino acid side chains.
+
At
the lysine side chain will contain a positive charge, NH 3CH 2CH 2CH 2CH 2 ¬ ,
and the aspartic acid side chain will contain a negative charge,
These two
side chains will be held together by an ionic bond:
+
¬ CH 2COO ⁄- NH 3CH 2CH 2CH 2CH 2 ¬
ionic bond
25.
The tripeptide, Gly-Ala-Thr, will
(a) react with
to give a violet color. The tripeptide has the required two peptide
bonds.
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(b)
(c)
not react to give a positive xanthoproteic test because there are no benzene ring
compounds in this tripeptide.
react with ninhydrin to give a blue solution. (Contains the required amino acids for
reaction.)
26.
The tripeptide, Gly-Ser-Asp, will
(a) react with
to give a violet color. The tripeptide has the required two peptide
bonds.
(b) not react to give a positive xanthoproteic test because there are no benzene ring
amino acids in this tripeptide.
(c) react with ninhydrin to give a blue solution. (Contains the required number of
amino acids for reaction.)
27.
Hydrolysis breaks the peptide bonds. One water molecule will react with each peptide
bond, a hydrogen atom attaches to the nitrogen to complete the amino group and an
¬ OH group attaches to the carboxyl carbon. The tripeptide, Ala-Phe-Asp, will
hydrolyze to yield the following:
COOH
ƒ
ƒ
CH2
CH3
CH2
ƒ
ƒ
ƒ
NH2CHCOOH+NH2CHCOOH+NH2CHCOOH
28.
Hydrolysis breaks the peptide bonds. One water molecule will react with each peptide
bond, a hydrogen atom attaches to the nitrogen to complete the amino group and an
¬ OH group attaches to the carboxyl carbon. The tripeptide, Ala-Glu-Tyr, will hydrolyze
to yield the following:
COOH
ƒ
CH2
ƒ
CH3
CH2
ƒ
ƒ
NH2CHCOOH+NH2CHCOOH+
OH
ƒ
ƒ
CH2
ƒ
NH2CHCOOH
29.
(
1 mol Fe
1 mol cytochrome c
((
55.85 g Fe
mol Fe
((
100. g cytochrome c
0.43 g Fe
( = 1.3 × 10
The molar mass of cytochrome c is 1.3 * 104 g> mol
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4
g
mol
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30.
(
4 mol Fe
1 mol hemoglobin
((
55.85 g Fe
mol Fe
((
100. g hemoglobin
0.33 g Fe
( = 6.8 × 10
4
g
mol
The molar mass of hemoglobin is 6.8 * 104 g> mol
31.
The amino acid sequence of the heptapeptide is:
Gly - Phe - Leu
Phe - Ala - Gly
Leu - Ala - Tyr
Phe - Ala - Gly - Phe - Leu - Ala - Tyr
32.
The amino acid sequence of the heptapeptide is:
Phe - Gly - Tyr
Ala - Leu - Phe
Phe - Ala - Ala
Phe - Ala - Ala - Leu - Phe - Gly - Tyr
33.
This newly discovered protein is probably a structural-support protein. The high
percentage of beta-pleated sheet means that there are many hydrogen bonds holding the
protein together in a very stable structure.
34.
This newly discovered protein is probably not a structural-support protein because it is
globular in shape and has secondary structure (beta pleated sheet) at its core. Thus, it is
more likely to be a binding protein.
35.
A domain is a compact piece of the overall protein structure that is relatively small (about
the size of myoglobin, for example). A protein with a molar mass of about 452,000
g/mole is likely to have many domains.
36.
A domain is a compact piece of protein structure of about 20,000 g/mole. The newly
discovered protein with two domains is more likely to have a molar mass between 40,000
and 60,000 g/mole.
37.
Alpha keratins have a high percentage of the alpha helix secondary structure. The alpha
helix is like a spring in that it is stretchable, so hair is stretchable.
38.
The silk protein, fibroin, has a high percentage of the secondary structure, beta-pleated
sheet. The secondary structure is like a sheet of paper in that it is flexible but not
stretchable. Thus, fibroin is not easily stretched.
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39.
The amino acid sequence of the nonapeptide is:
Arg - Pro
Pro - Pro
Pro - Gly - Phe
Phe - Ser
Ser - Pro - Phe
Phe - Arg
Arg - Pro - Pro - Gly - Phe - Ser - Pro - Phe - Arg
40.
A binding site has attractive forces and a specific shape that selectively binds a particular
biochemical.
41.
Most fibrous proteins provide structural support. For example, connective tissue (e.g.,
tendons), skin, and blood vessel walls all are strengthened by fibrous proteins.
42.
Transport proteins carry chemicals from one place to another. In general, motion proteins
move cells or organisms from one place to another. Hemoglobin is an example of a
transport protein that moves oxygen from the lungs to the tissues. Myosin is an example
of a motion protein that allows muscles to contract.
43.
The steroisomers of threonine:
COOH
COOH
ƒ
ƒ
H ¬ C ¬ NH 2
H 2N ¬ C ¬ H
ƒ
ƒ
H ¬ C ¬ OH
HO ¬ C ¬ H
ƒ
ƒ
CH 3
CH 3
44.
45.
COOH
ƒ
H ¬ C ¬ NH 2
ƒ
HO ¬ C ¬ H
ƒ
CH 3
COOH
ƒ
H 2N ¬ C ¬ H
ƒ
H ¬ C ¬ OH
ƒ
CH 3
The immunoglobulin hypervariable regions allow the body to produce millions of
different immunoglobulins. Each immunoglobulin has a unique antigen binding site and
two hypervariable regions with distinct amino acid sequences.
(a)
The structure of alanine at p
(b)
The structure of lysine at
CH 3
ƒ
would be NH 2CHCOO +
would be NH 3CH 2CH 2CH 2CH 2CHCOO ƒ
NH 3+
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(c)
The net charge on lysine at
in part (b)].
would be positive [see the structure of lysine
46.
Nineteen dipeptides can be written with glycine on the N-terminal side. Another nineteen
are possible with glycine on the C-terminal end. Finally, one dipeptide can be written
with two glycines giving a total of thirty-nine dipeptides.
47.
Vasopressin will have a higher isoelectric point than oxytocin. Vasopressin has two
different amino acids as compared with oxytocin, a phenylalanine instead of an isoleucine
and an arginine instead of a leucine. Thus, vasopressin has one additional basic amino
acid (arginine) which will cause the vasopressin isoelectric point to be higher than the
oxytocin isoelectric point.
48.
Leucine
(CH 3)2CHCH 2CHCOOH
ƒ
NH 2
Alanine
CH 3CHCOOH
ƒ
NH 2
Glutamic Acid
HOOCCH 2CH 2CHCOOH
ƒ
NH 2
Glutamic acid is the only one of these three amino acids with polar bonds in its side
chain. Thus, glutamic acid will be the most polar.
49.
(a)
OH
ƒ
OH
ƒ
ƒ
ƒ
CH2 O
CH2 O
ƒ
‘
ƒ
‘
H2N ¬ CH ¬ C ¬¬ NH ¬ CH ¬ C ¬ OH
(b)
COOH
H 2N ¬ C ¬ H
COOH
H ¬ C ¬ NH2
CH2
HO
HO
OH
L-dopa
(c)
(d)
CH2
OH
D-dopa
Dopamine does not have a chiral carbon and thus, does not exist as a pair of
stereoisomers.
Norepinephrine contains a primary amine while epinephrine contains a secondary
amine.
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