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CHAPTER 29
AMINO ACIDS, POLYPEPTIDES, AND PROTEINS SOLUTIONS TO REVIEW QUESTIONS 1.
The amino acids of proteins are called alpha amino acids because the amine group is always attached to the alpha carbon atom, that is, the carbon atom next to the carboxyl group, COOH.
⁄
NH 2 ƒ R ¬ C ¬ COOH ƒ H alpha carbon atom 2.
All amino acids and proteins contain carbon, hydrogen, oxygen, and nitrogen. Sulfur is contained in some of the amino acids, and thus in most proteins.
3.
Proteins from some foods are of greater nutritional value than others because they are “complete”, which means they contain all eight essential amino acids, those which the human body cannot synthesize.
4.
The amino acids which are essential to humans are isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine.
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)
(c) (d)
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. 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. - 451 -
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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.
The major structural difference between hemoglobin and myoglobin is that hemoglobin is composed of four subunits while myoglobin only contains one. Hemoglobin’s quaternary structure allows a more effective control of oxygen transport than is possible with myoglobin.
10.
Both the a-helix and b -pleated sheet are examples of secondary protein structures. The a-helix forms a tube composed of a spiraling polypeptide chain while the b -pleated sheet forms a plane composed of polypeptide chains aligned roughly parallel to each other.
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 CuSO4 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)
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.
16.
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.
17.
A prion is an incorrectly folded protein that causes other proteins to fold in the same way. A bacteria is a living organism that can reproduce itself.
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CHAPTER 29 SOLUTIONS TO EXERCISES 1.
D-alanine
L-alanine (form commonly found in proteins)
COOH ƒ H ¬ C ¬ NH 2 ƒ CH 3 2.
COOH ƒ H 2N ¬ C ¬ H ƒ CH 3
D-serine
L-serine (form commonly found in proteins)
COOH ƒ H ¬ C ¬ NH 2 ƒ CH 2OH 3. 4.
COOH ƒ H 2N ¬ C ¬ H ƒ CH 2OH
(6.0 g nitrogen) A 16 g nitrogen B A 100.0 g food product B (100) = 38% protein 100. g protein
1
(5.2 g nitrogen) A 16 g nitrogen B A 250.0 g hamburger B (100) = 13% protein 100. g protein
1
250.0 g hamburger A 100 g hamburger B = 33 g protein 13 g protein
5.
The structural formula for threonine at its isoelectric point is: CH 3 ¬ CH ¬ CH ¬ COO ƒ ƒ OH NH 3+
6.
The structural formula for asparagine at its isoelectric point is: O ‘ NH 2C ¬ CH 2 ¬ CH ¬ COO ƒ NH 3+
7.
For phenylalanine: (a) zwitterion formula CH2CHCOO– ƒ NH 3±
(b) formula in 0.1 M H 2SO4
(c) formula in 0.1 M NaOH
CH2CHCOOH ƒ NH 3±
CH2CHCOO– ƒ NH 2
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8.
For tryptophan: (a) zwitterion formula CH2CHCOO– ƒ NH 3± N H
9.
(c) formula in 0.1 M NaOH
CH2CHCOOH ƒ NH 3± N
CH2CHCOO– ƒ NH 2 N
H
H
Ionic equations showing how alanine acts as a buffer towards: (a) H + CH 3CHCOO - + H + ¡ CH 3CHCOOH ƒ ƒ NH 3+ NH 3+ (b)
10.
(b) formula in 0.1 M H 2SO4
OH -
CH 3CHCOO - + OH - ¡ CH 3CHCOO - + H 2O ƒ ƒ NH 3+ NH 2
Ionic equations showing how leucine acts as a buffer towards: (a) H + (CH 3)2CHCH 2CHCOO - + H + ¡ (CH 3)2CHCH 2CHCOOH ƒ ƒ NH 3+ NH 3+ (b)
OH -
(CH 3)2CHCH 2CHCOO - + OH - ¡ (CH 3)2CHCH 2CHCOO - + H 2O ƒ ƒ NH 3+ NH 2
11.
Methionine will have the following structure at its isoelectric point: CH 3SCH 2CH 2CHCOO ƒ NH 3+
12.
Valine will have the following structure at its isoelectric point: (CH 3)2CHCHCOO ƒ NH 3+
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13.
The two dipeptides containing serine and alanine: CH 2OH CH 3 CH 3 CH 2OH ƒ ƒ ƒ ƒ NH 2CH C ¬⁄ NHCHCOOH NH 2CH C ¬ NH C HCOOH ⁄ ‘ ‘ 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 2CH C ¬⁄ NHCH 2COOH ‘ ‘ O O peptide bond peptide bond Gly-Thr
Thr-Gly
H2 C 15.
H2C
H2 C CH2
HN
CH ¬ COOH
H2C HN
O H2C ‘ CH¬¬ C ¬¬¬ N CH2
Pro
16.
CH 2SH ƒ H 2N ¬ CH ¬ COOH
(a)
(b)
glycylglycine
alanylglycylserine
CH2 CH¬¬ COOH
Pro-Pro CH 2 ¬¬¬¬ S¬¬ S ¬¬¬¬ CH 2 ƒ ƒ H 2N ¬ CH ¬ COOH H 2N ¬ CH ¬ COOH
Cys 17.
H2 C
Cys-Cys NH 2CH 2C ¬ NHCH 2COOH ‘ O CH 3 CH 2OH ƒ ƒ NH 2CH C ¬ NHCH 2C ¬ NHCHCOOH ‘ ‘ O O
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(c)
18.
(a)
(b)
(c)
glycylserylglycine
alanylalanine
CH 2OH ƒ NH 2CH 2C ¬ NHCH C ¬ NHCH 2COOH ‘ ‘ O O
CH 3 CH 3 ƒ ƒ NH 2CH C ¬ NHCHCOOH ‘ O
serylglycylglycine
CH 2OH ƒ NH 2CH C ¬ NHCH 2C ¬ NHCH 2COOH ‘ ‘ O O
serylglycylalanine
CH 2OH CH 3 ƒ ƒ NH 2CH C ¬ NHCH 2C ¬ NHCHCOOH ‘ ‘ O O
19.
All the possible tripeptides containing one unit each of glycine, phenylalanine, and leucine: Gly-Phe-Leu Gly-Leu-Phe Phe-Gly-Leu Phe-Leu-Gly Leu-Gly-Phe Leu-Phe-Gly
20.
All the possible tripeptides containing one unit each of tyrosine, aspartic acid, and alanine: Tyr-Asp-Ala Tyr-Ala-Asp Asp-Tyr-Ala Asp-Ala-Tyr Ala-Tyr-Asp Ala-Asp- Tyr
21.
H O CH3 ƒ ƒ ‘ ¬C¬C¬N¬C¬ ƒ ƒ ƒ H H H
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22.
23.
H O CH3 ƒ ƒ ‘ ¬C¬C¬N¬C¬ ƒ ƒ ƒ H H H 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 ..... O ⁄ CH 2 ¬ hydrogen bond
24.
Tertiary protein structure is usually held together by bonds between amino acid side chains. +
At pH = 7, 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, -OOCCH 2 ¬ . 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 CuSO4 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 compounds in this tripeptide. (c) 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 CuSO4 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.)
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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 CH2 CH3 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 CH2 CH3 ƒ ƒ NH2CHCOOH+NH2CHCOOH+
OH ƒ
ƒ CH2 ƒ NH2CHCOOH
29.
A 1 mol cytochrome c B A mol Fe B A 55.85 g
1 mol Fe
100. g cytochrome c B 0.43 g Fe
g
= 1.3 * 104 mol
The molar mass of cytochrome c is 1.3 * 104 g>mol 30.
A 1 mol hemoglobin B A mol Fe B A 4 mol Fe
55.85 g
100. g hemoglobin B 0.33 g Fe
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
g
= 6.8 * 104 mol
Leu - Ala - Tyr
Phe - Ala - Gly - Phe - Leu - Ala - Tyr
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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.
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
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40.
(a) (b)
41.
Yes, all proteins have a primary structure (a sequence of amino acids linked by peptide bonds) but need not form regular, three dimensional secondary structures such as the a-helix or b -pleated sheet. No, all proteins must have a primary structure because, by definition, these molecules are polymers composed of a sequence of amino acids linked by peptide bonds (a primary structure).
42.
A small protein like ribonuclease (or myoglobin) would have a small number of protein domains, probably only one. Small proteins (e.g., myoglobin, ribonuclease) commonly fold into one globular unit (one domain) while larger proteins will fold into more than one globular unit (more than one domain).
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.
Arginine will not migrate to either electrode in an electrolytic cell at a pH of 10.8. Arginine will migrate towards the positive electrode at pH greater than 10.8, that is, more basic than its isoelectric point.
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 with two distinct amino acid sequences and unique antigen binding sites.
(a)
CH 3 ƒ The structure of alanine at pH = 9.0 would be NH 2CHCOO +
46.
(b)
The structure of lysine at pH = 9.0 would be NH 3CH 2CH 2CH 2CH 2CHCOO ƒ NH 3+
(c)
The net charge on lysine at pH = 9.0 would be positive [see the structure of lysine in part (b)].
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. - 461 -
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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
COOH H2N ¬ C ¬ H
H ¬ C ¬ NH2 CH2
CH2 HO
HO OH L-dopa
(c) (d)
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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