Deck 18: Amino Acids and Proteins

Question 1

Glutamic acid has an isoelectric point of 3.08. At which pH is the cationic form in greatest concentration?

A) 2
B) 3.2
C) 5.6
D) 9.7

Answer 1

2

Question 2

Which is the charge on lysine at pH 11?

A) 0
B) +1
C) -1
D) +2

Answer 2

-1

Question 3

Which amino acid has a nonpolar side chain?

A) I
B) II
C) III
D) IV

Answer 3

II

Question 4

Which is the chemical structure of the tripeptide glutathione (glu-cys-gly)?

A) I
B) II
C) III
D) IV

Question 5

Lysine has an isoelectric point of 9.74. What charge does tyrosine have at pH 7 and toward which electrode would it migrate during electrophoresis?

A) negative, anode
B) positive, cathode
C) negative, cathode
D) positive, anode

Question 6

Which is the order of increasing acidity for the indicated carboxyl groups (least first)?

A) I, II, III
B) II, III, I
C) III, II, I
D) I, III, II

Question 7

Which amino acid has a basic side chain?

A) I
B) II
C) III
D) IV

Question 8

Isoleucine has pk_a values of 2.32 (-COOH) and 9.76 (-NH₃⁺). Which is isoleucine's isoelectric point?

A) 3.08
B) 7.64
C) 6.04
D) 9.74

Question 9

Tyrosine has an isoelectric point of 5.63. What charge does tyrosine have at pH 7 and toward which electrode would it migrate during electrophoresis?

A) negative, anode
B) positive, cathode
C) negative, cathode
D) positive, anode

Question 10

Which amino acids have protic side chains?

A) I, III
B) II, IV
C) II, III
D) III, IV

Question 11

Which is the predominant form of lysine in blood plasma at pH 7.4?

A) I
B) II
C) III
D) IV

Question 12

Which describes the isoelectric point of an amino acid?

A) The degree of ionization of the amino acid at pH 7.
B) The pH at which there is no net charge for the amino acid.
C) The degree of ionization of the amino acid at pH 7 in an electric field.
D) The pH at which the amino acid has a maximal charge.

Question 13

Which molecule has an overall positive charge?

A) I
B) II
C) III
D) IV

Question 14

Which is the order of increasing mobility of the molecule toward the cathode (least first)?

A) III, I, II, IV
B) I, III, II, IV
C) IV, II, I, III
D) III, IV, I, II

Question 15

Which characteristics are correct for a peptide bond in a polypeptide?
I. planar
II. cis
III. trans
IV. tetrahedral

A) I, II
B) I, III
C) II, IV
D) III, IV

Question 16

Arginine has an isoelectric point of 10.76. At which pH would the predominate form of arginine in solution migrate toward the positive terminal during electrophoresis?

A) 5
B) 7
C) 10.76
D) 12

Question 17

Which is the structure of the pentapeptide that gave lys-leu-phe on reaction with cyanogen bromide, and gave fragments met-lys, leu-phe, and arg on reaction with trypsin.

A) arg-met-phen-leu-lys
B) lys-leu-phe-arg-met
C) arg-met-lys-leu-phe
D) met-arg-lys-leu-phe

Question 18

Which is the order of increasing basicity for the indicated amino groups (least first)?

A) I, II, III
B) II, III, I
C) III, II, I
D) I, III, II

Question 19

Which is the charge of lysine at pH 2?

A) 0
B) +1
C) -1
D) +2

Question 20

Aspartic acid has an isoelectric point of 2.98. At which pH would the predominant form of aspartic acid in solution migrate toward the negative electrode during electrophoresis?

A) 1
B) 2.98
C) 4
D) 7

Question 21

Spider silk is remarkably strong, its tensile strength is superior to that of steel and it is extremely lightweight: a strand of spider-silk long enough to circle the earth would weigh less than 500 g. In a typical spider silk strand, crystalline beta-sheet regions, which are rich in glycine- and alanine, alternate with amorphous segments. The latter are responsible for the sticky or non-sticky properties, depending on the kind of spider silk. Why are glycine and alanine especially suited for the formation of beta-sheet regions?
I. Glycine and alanine are hydrophobic and cause the hydrophobic sticking of neighboring polymer strands.
II. Glycine and alanine feature very little or no steric hindrance for the formation of hydrogen bonds between neighboring protein strands.
III. Glycine and alanine feature very little or no steric hindrance for the formation of hydrogen bonds within a protein strands.
IV. Glycine and alanine are polar. They allow ionic interactions between neighboring polymer chains.

A) I and II are correct
B) II and III are correct
C) I and III are correct
D) II and IV are correct

Question 22

The structure of a common amino acid with a polar side chain is

Question 23

Karl Nessler received the patent for the so-called "hot procedure" for a permanent (hair) in 1906. The hair was treated with a basic solution (NaOH in water, pH approx. 10) and then heated for several hours on the curler. The result was often extremely curly hair. What kind of bonds was/were actually (partially) broken and reformed?
I. hydrogen bonds
II. ionic bonds
III. disulfide-bridges
IV. dipolar bonds

A) I and II are correct
B) I, II and III are correct
C) I, II, and IV are correct
D) all of the above are correct

Question 24

Denaturation is a process in which proteins lose their natural shape and order of assembly and, therefore, their biological functions. Which of the following statements is/are true?
I. In quaternary structure denaturation, protein sub-units are dissociated.
II. In tertiary structure denaturation, covalent and ionic bonds are predominantly formed.
III. In tertiary structure denaturation, covalent and ionic bonds are disrupted.
IV. In quaternary structure denaturation, proteins lose all regular repeating patterns, such as alpha-helices and beta-pleated sheets.

A) I and II are correct
B) II and III are correct
C) I and III are correct
D) II and IV are correct

Question 25

The tertiary structure of proteins depends primarily on which property of amino acids?
I. disulfide bonds
II. hydrogen bonds
III. amide bonds
IV. polar side chains

A) III, IV
B) I, IV
C) II, III
D) I, II

Question 26

A pentapeptide has the following proportions of amino acids: gly (1), leu (1), val (1), phe (2). Treatment of the pentapeptide with chymotrypsin gave the following fragments: gly-val, leu, phe. Which is the structure of the pentapeptide?

A) phe-phe-gly-val-leu
B) gly-val-phe-leu-phe
C) leu-gly-val-phe-phe
D) phe-leu-gly-val-phe

Question 27

Denaturation is a process in which proteins lose their natural shape and order of assembly and, therefore, their biological functions. Which of the following statements is/are true?
I. In secondary denaturation, some of the amide-bonds of the proteins´ backbones are hydrolyzed.
II. In secondary structure denaturation, proteins lose all regular repeating pattern, such as alpha-helices and beta-pleated sheets.
III. In secondary structure denaturation, proteins adopt random-coil conformations.
IV. In secondary structure denaturation, noncovalent dipole-dipole interactions between polar amino acids/side chains and the solvent are disrupted.

A) I and II are correct
B) II and III are correct
C) I and III are correct
D) II and IV are correct

Question 28

Oxytocine is a mammalian hormone that also acts as a neurotransmitter in the brain. Among many other functions, it also facilitates birth and breastfeeding. Oxytocine is a small peptide made of nine amino acids (a nonapeptide). The primary sequence is cysteine - tyrosine - isoleucine - glutamine - asparagine - cysteine - proline - leucine - glycine. In its active form oxytocine forms a cyclic structure. Which secondary bond is most suitable to form the cyclic structure?

A) a thioester between cysteine and glycine
B) a disulfide bridge between cysteine and cysteine
C) an amide between cysteine and glycine
D) an ester between the phenolic group of tyrosine and glycine

Question 29

Urokinase-type Plasminogen Activator (uPa) is a serine endopeptidase. The active site of this peptidase binds the peptide-motif Ser-Gly-Arg-Ser-Ala and cleaves the protein/peptide between arginine and serine. What is the sequence of the products of the oligopeptide
Ala-Gly-Ser-Gly-Arg-Ser-Ala-Lys-Gly-Ala-Ser-Asp
After cleavage by uPa?

A) Ala-Gly and Ser-Gly-Arg-Ser-Ala-Lys-Gly-Ala-Ser-Asp
B) Ala-Gly-Ser-Gly-Arg and Ser-Ala-Lys-Gly-Ala-Ser-Asp
C) Ala-Gly-Ser-Gly-Arg-Ser-Ala-Lys-Gly-Ala-Ser and Asp
D) Ala-Gly-Ser-Gly-Arg-Ser and Ala-Lys-Gly-Ala-Ser-Asp

Question 30

What are the differences between polyamides and proteins ?
I. Polyamides are unable to undergo hydrogen bonding between individual polymer chains.
II. Polyamides usually do not have hydroxyl- or thiol-groups as side chains.
III. Proteins and polyamides can be partially crystalline.
IV. Polyamides have a more stable bond between their monomers than proteins have between the individual amino acids.

A) I and II
B) II and III
C) II and IV
D) III and IV

Question 31

Serotonin regulates intestinal movements in humans, as well as the human mood, appetite, and some cognitive functions including memory and learning. In the human body, serotonin is synthesized by hydroxylation of the essential amino acid L-tryptophan and subsequent decarboxylation. Complete the following reaction scheme:

Question 32

The structure of a common amino acid with a basic side chain is

Question 33

A polypeptide gave the following proportions of amino acids upon hydrolysis: ala (1), gly (1), ile (2), phe (2), ser (1), tyr (2). Edman degradation yields tyrosine phenylthiohydantoin. Partial hydrolysis of the peptide gave a mixture of smaller peptides including: ala-gly, gly-tyr, ile-ile, phe-ile, ser-phe, tyr-ser, tyr-phe, ile-ala. Which is the C-terminal amino acid in the original peptide?

A) tyr
B) ser
C) phe
D) ile

Question 34

Which are true describing the secondary structure of a protein that is an $\alpha$ -helix?
I. The helix is coiled counterclockwise.
II. The N-H bond and the C=O bond point outward.
III. Hydrogen bonding is between groups 4 amino acid units apart.
IV. The coil has 3.6 amino acids per turn.

A) I, II
B) I, III
C) II, IV
D) III, IV

Question 35

The structure of vasopressin is very similar to that of oxytocin (primary sequence of vasopressin: cysteine - tyrosine - phenylalanine - glutamine - asparagine - cysteine - proline - arginine - glycine), which is also a nonapeptide with a disulfide bridge. One of the most important roles of vasopressin is to regulate the body's retention of water; it is released when the body is dehydrated and causes the kidneys to conserve water, thus concentrating the urine, and reducing urine volume. In addition, it has a variety of neurological effects on the brain. What are the differences in the structures of vasopressin and oxytocin?
I. residue #3: isoleucine (oxytocin) vs. phenylalanine (vasopressin)
II. residue #7: isoleucine (oxytocin) vs. phenylalanine (vasopressin)
III. residue #8: leucine (oxytocin) vs. arginine (vasopressin)
IV. residue #4: asparagine (oxytocin) vs. cysteine (vasopressin)

A) I and II are correct
B) II and III are correct
C) I and III are correct
D) II and IV are correct

Question 36

The first known procedures to bend straight hair into curls dates from 3000 B.C.: Hot Curlers made from clay were used. The hair was apparently dry. What kind of bonds was/were actually broken and reformed?

A) hydrogen bonds
B) ionic bonds
C) disulfide-bridges
D) dipolar bonds

Question 37

Draw both L-aspartic acid and D-aspartic acid. Specify the configuration (R or S) at each stereocenter.

Question 38

Why will Gly-Met-Gly react with cyanogen bromide, but Gly-Cys-Gly will not react with cyanogen bromide?
I. There would be a highly strained four-membered ring intermediate in the case of cysteine.
II. After the addition of the thiol of cysteine to the cyano-group, a stable thioether will be formed, which does not react any further.
III. After the addition of the thiol of cysteine to the bromo-cation, a stable thioether will be formed, which does not react any further.
IV. Cysteine cannot form a stable bromonium-ion intermediate.

A) I and II are correct
B) II and III are correct
C) I and III are correct
D) II and IV are correct

Question 39

The secondary structure of proteins depends primarily on which property of amino acids?

A) disulfide bonds
B) hydrogen bonds
C) amide bonds
D) polar side chains

Question 40

The structure of a common amino acid with an acidic side chain is

Question 41

The isoelectric point of cysteine is ______________.
pKa (COOH) = 2.05, pKa (NH₃⁺) = 10.25, pKa (SH) = 8.00

Question 42

The result of the reaction of the hydrolysis of Leu-Ile-Lys-Cys-Val-Asn-Gln-Tyr with trypsin is __________________________.

Question 43

The isoelectric point of Glycine is 6.06 (pKa (COOH) = 2.35, pKa (NH₃⁺) = 9.78).

Question 44

The sequence of a heptapeptide can be deduced from the following experimental results as Thr-Tyr-Cys-Gln-Arg-Trp-His
Edman degradation Thr
Hydrolysis catalyzed by Trypsin Thr-Tyr-Cys-Gln-Arg
Trp-His
Hydrolysis catalyzed by Chymotrypsin Thr-Tyr
Cys-Gln-Arg-Trp
His

Question 45

Whereas L-cysteine is a building block of peptides and proteins, D-cysteine is a common building block of bacterial membranes. Draw both, L-cysteine and D-cysteine. Which stereocenter has S and which has R configuration?

Question 46

$\alpha$ -Helix and $\beta$ -sheet are examples of protein secondary structure.

Question 47

The sequence of an octapeptide can be deduced from the following experimental results as Cys-Asn-Met-Tyr-Val-Phe-Lys-Pro.
Edman degradation Cys
Hydrolysis catalyzed by Trypsin Cys-Asn-Met-Tyr-Val-Phe-Lys
Pro
Hydrolysis catalyzed by Chymotrypsin Cys-Asn-Met-Tyr
Val-Phe
Lys-Pro
Treatment with Cyanogen Bromide Cys-Asn-Met
Tyr-Val-Phe-Lys-Pro

Question 48

The structure of the tripeptide Glu-Gly-Phe is

Question 49

Arginine is an amino acid with a basic side chain.

Question 50

The result of the reaction of the hydrolysis of Ala-Phe-Leu-Tyr-Leu-Pro with chymotrypsin is __________________________.

Question 51

The sequence of a decapeptide can be deduced from the following experimental results as Leu-Met-Ser-Thr-Trp-His-Phe-Asp-Lys-Glu.
Edman degradation Leu
Hydrolysis catalyzed by Trypsin Leu-Met-Ser-Thr-Trp-His-Phe-Asp-Lys
Glu
Hydrolysis catalyzed by Chymotrypsin Leu-Met-Ser-Thr-Trp
His-Phe
Asp-Lys-Glu
Treatment with Cyanogen Bromide Leu-Met
Ser-Thr-Trp-His-Phe-Asp-Lys-Glu

Question 52

A major stabilizing factor of protein tertiary structure is disulfide linkages.

Question 53

Asparagine is an amino acid with an acidic side chain.

Question 54

Complete the following mechanism

Question 55

At pH 7.05 lysine pI = 9.74) will migrate toward the positive electrode during electrophoresis.

Question 56

The result of the reaction of Asp-Val-Met-Leu-His with cyanogen bromide is _______________________.

Question 57

Which of the following amino acids react with more than one equivalent of phenylisothiocyanate in an Edman-reaction? Assume that all four are in an N-terminal position.

Question 58

Complete the following mechanism:

Question 59

The isoelectric point of proline is ______________.
pKa (COOH) = 2.00, pKa (NH₃⁺) = 10.60