Exam 1

Front 1

The significance of Ainfinsen's renaturation experiment with urea and 2-mercaptoethanol demonstrated that the ________ structure species how the protein should fold into its three-dimensional structure.

Back 1

Primary

Front 2

The entropy of water molecules ___________ when the hydrophobic residues become buried within the protein molecule.

Back 2

Increase

Front 3

Changing Arg to Asp in a protein is considered to be a _____________ amino acid substitution.

Back 3

nonconservative

Front 4

A negative hydropathy index value of negative exergonic free energy transfer indicates a region of a polypeptide sequence that is ____________.

Back 4

Hydrophilic

Front 5

Noncovalent interactions formed between many groups wihtin a folded protein yield a ______ deltaH that contributes to stabilization of the folded structure

Back 5

Negative

Front 6

Two identical subunits or protomers can be superimposed by ______________ symmetry.

Back 6

cyclic

Front 7

A polypeptide often folds into two or more stable globular units that are called ____________. These globular units often have distinct functions in a polypeptide.

Back 7

Domains

Front 8

Organic solvent such as ethanol is a denaturing agent that disrupt _______ between protein groups.

Back 8

H-bonds

Front 9

Proline and glycine residues are most likely to occur in which of the following structures?
a. an alpha-helix
b. a beta-sheet
c. a beta-turn
d. a coiled coil

Back 9

c. a beta-turn

Front 10

An alpha-helix would be destabilized most by: ______
a. an electric dipole spanning several peptide bonds throughout the alpha helix.
b. the presence of Lys residues near the amino terminus of the alpha helix.
c. the presence of an Arg residue near the carboxyl terminus of th alpha helix.
d. the presence of Asn or Gln whose side chains can form H-bonds with bare N-H and C=O groups found in the last four residues at each end of the alpha-helix

Back 10

b. The presence of Lys residues near the amino terminus of the alpha-helix.

Front 11

What is the overall net charge on the peptide Lys-Lys-Ser-Glu at pH 7? Given Lysine has a pKa alpha-COOH = 2.16, pKa alpha-NH3+=9.06, and pKr=10.54(epsilon-NH3+) and Glutamic acid has a pKa alpha-COOH=2.10, alpha-NH3+=9.47, pKr=4.07 (gamma-COOH).

a. +2
b. +1
c. -1
d. -2

Back 11

b. +1

Front 12

The blood clotting protein Fibrinogen has a pI of 5.5 and can be precipitated out with 0.8 M ammonium sulfate. Which of the following is true?

a. At pH 5.5, the protein will be more soluble in an aqueous buffer than at other pH values.
b. The protein will be more soluble in aqueous buffer if 1.6 M ammonium sulfate is added.
c. At pH 5.5, the protein will more likely precipitate out of solution.
d. The protein's solubility will depend upon its size.

Back 12

c. At pH 5.5, the protein will more likely precipitate out of solution.

Front 13

All of the statements about the peptide Val-Asp-Trp-Asn-Ser are correct EXCEPT:

a. Dansyl chloride will react with serine and yield a dansylated serine residue.
b. This polypeptide would absorb ultraviolet radiation at 280 nm.
c. After the second round of Edman degradation using the reagent PITC, the PTH-amino acid residue released would be PTH-Asp.
The peptide cannot be chemically cleaved using cyanogen bromide (CNBr)

Back 13

a. Dansyl chloride will react with serine and yield a dansylated serine residue.

Front 14

You are interested in sequencing a protein hormone that contains two short polypeptide chains linked by two interstrand disulfide bonds. The most logical order of events to perform in order to sequence this protein would be:
A: The peptides are reduced with mercaptoethanol
B: The peptides are sequenced using Edman degradation
C: The peptides are fragmented by specific proteases.
D: The peptides are alkylated with iodoacetamide.

a. C,A,D,B
b. C,B,A,D
c. A,C,D,B
d. A,D,C,B

Back 14

d. A,D,C,B

Front 15

Treatment of the following peptide with the endopeptidase Trypsin will yield ________ peptides.
Met-Phe-Tyr-Arg-Pro-Gly-Lys-Ser-Leu-Arg

a. two
b. three
c. four
d. five

Back 15

a. two

Front 16

Bicarbonate is the most significant buffer compound in the human blood. Inhaling and exhaling CO2 can adjust the blood pH. What effect does the expiration of CO2 from the lungs have on the blood pH?

a. It will cause an increase in dissociation of H2CO3 --> H+ + HCO3- and a drop in pH.
b. It will cause association of H+ and HCO3- --> H2CO3 and an increase in pH.
c. It will cause association of H+ and HCO3- --> H2CO3 and a decrease in pH.
d. Exhaling CO2 from the lungs will have no effect on the blood pH.

Back 16

b. It will cause association of H+ and HCO3- --> H2CO3 and an increase in pH.

Front 17

From the data shown below, which of the following statements correctly describes the subunit composition of the protein?

Molecular mass by gel-filtration: 100 kDa
Molecular mass by SDS-PAGE: 50 kDa
Molecular mass by SDS-PAGE with 2-mercaptoethanol: 25 kDa

a. The protein contains two 50 kDa subunits held together by disulfide bonds.
b. The protein contains four 25 kDa subunits all held together by disulfide bonds.
c. The protein contains two 50 kDa subunits held together by noncovalent forces and each 50 kDa subunit contains two 25 kDa subunits that are paired by disulfide bonds.
d. The protein contains four 25 kDa subunits held together only by noncovalent forces.

Back 17

c. The protein contains two 50 kDa subunits held together by noncovalent forces and each 50 kDa subunit contains two 25 kDa subunits that are paired by disulfide bonds.

Front 18

10. You have a mixture of 3 proteins with the following pIs:

Protein A: pI=7.0
Protein B: pI=9.0
Protein C: pI=5.0

At pH=8.0 you chromatograph them using an anion exchange column, with gradient of NaCl to elute proteins. What will be the order of elution?

a. C, A, then B
b. B, A, then C
c. A, C, then B
d. B, C, then A

Back 18

b. B, A, then C

Front 19

Hemoglobin has an isoelectric point of 6.9. What will be th electrophoretic behavior of this protein at pH 7.5 on an isoelectric focusing gel?

a. Hemoglobin protein molecules will distribute randomly throughout the gel when an electric field is applied.
b. Hemoglobin will stabilize in the gel at pH 7.5 and will not migrate in either direction.
c. Hemoglobin will have a negative charge and move toward the positive anode end until it reaches its pI.
d. Hemoglobin will have a positive charge and move towards the negative cathode end until it reaches its pI.

Back 19

c. Hemoglobin will have a negative charge and move toward the positive anode end until it reaches its pI.

Front 20

In the polypeptide (not pictured, sorry) rotation is possible around the _____.

a. C-N bond and C(alpha)-N
b. C(alpha)-C bond and C(alpha)-N bond
c. C-N bond and C(alpha)-C bond
d. C-N bond and C-C bond

Back 20

b. C(alpha)-C bond and C(alpha)-N bond

Front 21

Which of the following statements about beta-sheets is FALSE?

a. The side chains in a beta-sheet alternate between the two sides of the sheet.
b. The beta-sheet contains hydrogen bonds between the carbonyl oxygen of one residue and an amide hydrogen of a residue on an adjacent strand.
c. The hydrogen bonds of parallel beta-sheets are bent and less stable than antiparallel beta-sheets.
d. Antiparallel beta-sheets distribute hydrophobic side chains on both sides of the sheet.

Back 21

d. Antiparallel beta-sheets distribute hydrophobic side chains on both sides of the sheet.

Front 22

Which of these amino acids will form an alpha-helix?

a. poly L-lysine at pH 7
b. polyproline at pH 7
c. poly L-lysine at pH 2
d. poly L-aspartic acid at pH 2

Back 22

d. Poly L-aspartic acid at pH 2

Front 23

In a globular protein, one would expect to find a(n) ___________ residue located on the surface of the protein and a(n) __________ residue buried inside.

a. arginine, methionine
b. phenylalanine, asparagine
c. asparagine, serine
d. valine, leucine

Back 23

a. arginine, methionine

Front 24

The three dimensional structure for flavodoxin in shown below. Which of the following statements best describes the structure of this protein? (picture on test)

a. Each beta-sheet is parallel to the alpha-helix.
b. The structure has 2 layers of polypeptide backbone structure separated by 1 layer of hydrophobic region.
c. Both sides of the parallel beta-sheets are arranged with hydrophobic residues that are protected from the solvent by alpha-helices.
d. The beta-sheets are surrounded by alpha-helices that are antiparallel to each other.

Back 24

c. Both sides of the parallel beta-sheets are arranged with hydrophobic residues that are protected from the solvent by alpha-helices.

Front 25

Which of the following is NOT a feature of the alpha-keratin coiled-coil?

a. Covalent disulfide bonds can further stabilize the coiled-coil structure.
b. Alpha-keratin is mostly composed of hydrophobic residues.
c. The surfaces where the two alpha-helices touch are made up of hydrophobic amino acid residues.
d. The glycine side chain is important in close packing of the helical coiled coil.

Back 25

d. The glycine side chain is important in close packing of the helical coiled coil.

Front 26

Which of the following statement about the structure of collagen is FALSE?

a. Hydrogen bonds between the -NH of each Gly residue with the O=C of the adjacent Proline residue.
b. In the Collagen repeating sequence (Gly-X-Y)n, 5-hydroxylysine (Hyl), Lys, or His are present at a few of the X and Y positions.
C. The collagen fibrils are further strengthened and stabilized by intermolecular and intramolecular covalent crosslinks between lysine and proline residues.
d. Modification of proline and lysine residues occurs after the alpha polypeptide chains are synthesized using the enzyme prolyl hydroxylase and lysyl hydroxylase.

Back 26

c. The collagen fibrils are further strengthened and stabilized by intermolecular and intramolecular covalent crosslinks between lysine and proline residues.

Front 27

Describe the mechanism by which Hsp70 along with cochaperone protein Hsp40 and the GroEL/ES chaperonins assist in protein folding.

Back 27

When a polypeptide is being sequenced from mRNA by ribosomes, the nascent polypeptide has hydrophobic regions that become shileded by Hsp70 and Hsp40 by hydrophobic interactions to prevent the hydrophobic residues from unfavorably interacting with the hydrophilic solvent in the cytoplasm. The polypeptide is then transfered to the GroEL/ES chaperonin where the hydrophobic regions interact with the hydrophobic apical domain of GroEL. The GroES cap then interacts with the apical GroEL domain to trigger a conformational change to push the polypeptide into the hydrophilic core of GroEL. The protein, to avoid contact with the hydrophilic residues lining the core of GroEL. The ATP bound to the cis GroEL is hydrolyzed to ADP+Pi bound to the cis GroEL is released, also releasing the GroES cap. If the protein is properly folded, with the hydrophobic residues in the core, the protein is released. If not properly folded, the hydrophobic residues of the protein interact with the apical domain of GroEL and the cycle repeats.

Front 28

When a protein is synthesized, it is crucial that for the protein to fold into the correct three-dimensional structure in a reasonably short time. To sample all possible conformations would require over 10^70 years. Describe the folding process for a protein. What occurs during the folding process and what are the interactions that are driving the folding process?

Back 28

The primary amino acid sequence begins to fold into its secondary structure with the backbone forming hydrogen bonds with itself -- the side chains do not participate in the secondary structure. The secondary structure, including alpha-helices and/or beta-sheets, then undergoes hydrophobic collapse where hydrophobic regions come together by hydrophobic interactions. The protein is now a molten globule of secondary structures without a tertiary structure. Supersecondary structures begin to form driven by noncovalent interactions. Finally, tertiary structures are formed by non-covalent side chain interacttions (a covalent disulfide bond may also form in extracellular proteins after proper folding). The folding of the tertiary structure pushes water out of the hydrophobic core of the protein, completing the folding process.